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4G1I.cif
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4G1I.cif
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data_4G1I
#
_entry.id 4G1I
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 4.031
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
PDB 4G1I
RCSB RCSB073619
#
loop_
_database_PDB_rev.num
_database_PDB_rev.date
_database_PDB_rev.date_original
_database_PDB_rev.status
_database_PDB_rev.replaces
_database_PDB_rev.mod_type
1 2013-05-08 2012-07-10 ? 4G1I 0
2 2013-05-22 ? ? 4G1I 1
#
_database_PDB_rev_record.rev_num 2
_database_PDB_rev_record.type JRNL
_database_PDB_rev_record.details ?
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.db_id
_pdbx_database_related.details
_pdbx_database_related.content_type
PDB 3GR0 'Alternative crystal form' unspecified
PDB 3GR1 'Alternative crystal form' unspecified
PDB 4G08 . unspecified
PDB 4G2S . unspecified
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 4G1I
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.SG_entry ?
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.methods_development_category ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Bergeron, J.R.C.' 1
'Worrall, L.J.' 2
'Strynadka, N.C.J.' 3
#
_citation.id primary
_citation.title
'A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly.'
_citation.journal_abbrev 'Plos Pathog.'
_citation.journal_volume 9
_citation.page_first e1003307
_citation.page_last e1003307
_citation.year 2013
_citation.journal_id_ASTM ?
_citation.country US
_citation.journal_id_ISSN 1553-7366
_citation.journal_id_CSD ?
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 23633951
_citation.pdbx_database_id_DOI 10.1371/journal.ppat.1003307
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
primary 'Bergeron, J.R.' 1
primary 'Worrall, L.J.' 2
primary 'Sgourakis, N.G.' 3
primary 'Dimaio, F.' 4
primary 'Pfuetzner, R.A.' 5
primary 'Felise, H.B.' 6
primary 'Vuckovic, M.' 7
primary 'Yu, A.C.' 8
primary 'Miller, S.I.' 9
primary 'Baker, D.' 10
primary 'Strynadka, N.C.' 11
#
_cell.entry_id 4G1I
_cell.length_a 264.432
_cell.length_b 33.380
_cell.length_c 48.530
_cell.angle_alpha 90.00
_cell.angle_beta 91.60
_cell.angle_gamma 90.00
_cell.Z_PDB 8
_cell.pdbx_unique_axis ?
_cell.length_a_esd ?
_cell.length_b_esd ?
_cell.length_c_esd ?
_cell.angle_alpha_esd ?
_cell.angle_beta_esd ?
_cell.angle_gamma_esd ?
#
_symmetry.entry_id 4G1I
_symmetry.space_group_name_H-M 'C 1 2 1'
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.Int_Tables_number ?
_symmetry.space_group_name_Hall ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.details
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.pdbx_ec
1 polymer man 'Protein prgH' 26473.191 2 ? ? 'UNP residues 170-392' ?
2 non-polymer syn 'PENTAETHYLENE GLYCOL' 238.280 4 ? ? ? ?
3 non-polymer syn 'PHOSPHATE ION' 94.971 4 ? ? ? ?
4 water nat water 18.015 233 ? ? ? ?
#
loop_
_entity_keywords.entity_id
_entity_keywords.text
1 ?
2 ?
3 ?
4 ?
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code
;GSHMAAELDSLLGQEKERFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAY
YRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTF
VIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELKDDWLKGRSFQYGAEGYIKMSPGHWYFPSPL
;
_entity_poly.pdbx_seq_one_letter_code_can
;GSHMAAELDSLLGQEKERFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEENKRISIWLDTYYPQLAY
YRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSVNITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTF
VIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELKDDWLKGRSFQYGAEGYIKMSPGHWYFPSPL
;
_entity_poly.pdbx_strand_id A,B
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 GLY n
1 2 SER n
1 3 HIS n
1 4 MET n
1 5 ALA n
1 6 ALA n
1 7 GLU n
1 8 LEU n
1 9 ASP n
1 10 SER n
1 11 LEU n
1 12 LEU n
1 13 GLY n
1 14 GLN n
1 15 GLU n
1 16 LYS n
1 17 GLU n
1 18 ARG n
1 19 PHE n
1 20 GLN n
1 21 VAL n
1 22 LEU n
1 23 PRO n
1 24 GLY n
1 25 ARG n
1 26 ASP n
1 27 LYS n
1 28 MET n
1 29 LEU n
1 30 TYR n
1 31 VAL n
1 32 ALA n
1 33 ALA n
1 34 GLN n
1 35 ASN n
1 36 GLU n
1 37 ARG n
1 38 ASP n
1 39 THR n
1 40 LEU n
1 41 TRP n
1 42 ALA n
1 43 ARG n
1 44 GLN n
1 45 VAL n
1 46 LEU n
1 47 ALA n
1 48 ARG n
1 49 GLY n
1 50 ASP n
1 51 TYR n
1 52 ASP n
1 53 LYS n
1 54 ASN n
1 55 ALA n
1 56 ARG n
1 57 VAL n
1 58 ILE n
1 59 ASN n
1 60 GLU n
1 61 ASN n
1 62 GLU n
1 63 GLU n
1 64 ASN n
1 65 LYS n
1 66 ARG n
1 67 ILE n
1 68 SER n
1 69 ILE n
1 70 TRP n
1 71 LEU n
1 72 ASP n
1 73 THR n
1 74 TYR n
1 75 TYR n
1 76 PRO n
1 77 GLN n
1 78 LEU n
1 79 ALA n
1 80 TYR n
1 81 TYR n
1 82 ARG n
1 83 ILE n
1 84 HIS n
1 85 PHE n
1 86 ASP n
1 87 GLU n
1 88 PRO n
1 89 ARG n
1 90 LYS n
1 91 PRO n
1 92 VAL n
1 93 PHE n
1 94 TRP n
1 95 LEU n
1 96 SER n
1 97 ARG n
1 98 GLN n
1 99 ARG n
1 100 ASN n
1 101 THR n
1 102 MET n
1 103 SER n
1 104 LYS n
1 105 LYS n
1 106 GLU n
1 107 LEU n
1 108 GLU n
1 109 VAL n
1 110 LEU n
1 111 SER n
1 112 GLN n
1 113 LYS n
1 114 LEU n
1 115 ARG n
1 116 ALA n
1 117 LEU n
1 118 MET n
1 119 PRO n
1 120 TYR n
1 121 ALA n
1 122 ASP n
1 123 SER n
1 124 VAL n
1 125 ASN n
1 126 ILE n
1 127 THR n
1 128 LEU n
1 129 MET n
1 130 ASP n
1 131 ASP n
1 132 VAL n
1 133 THR n
1 134 ALA n
1 135 ALA n
1 136 GLY n
1 137 GLN n
1 138 ALA n
1 139 GLU n
1 140 ALA n
1 141 GLY n
1 142 LEU n
1 143 LYS n
1 144 GLN n
1 145 GLN n
1 146 ALA n
1 147 LEU n
1 148 PRO n
1 149 TYR n
1 150 SER n
1 151 ARG n
1 152 ARG n
1 153 ASN n
1 154 HIS n
1 155 LYS n
1 156 GLY n
1 157 GLY n
1 158 VAL n
1 159 THR n
1 160 PHE n
1 161 VAL n
1 162 ILE n
1 163 GLN n
1 164 GLY n
1 165 ALA n
1 166 LEU n
1 167 ASP n
1 168 ASP n
1 169 VAL n
1 170 GLU n
1 171 ILE n
1 172 LEU n
1 173 ARG n
1 174 ALA n
1 175 ARG n
1 176 GLN n
1 177 PHE n
1 178 VAL n
1 179 ASP n
1 180 SER n
1 181 TYR n
1 182 TYR n
1 183 ARG n
1 184 THR n
1 185 TRP n
1 186 GLY n
1 187 GLY n
1 188 ARG n
1 189 TYR n
1 190 VAL n
1 191 GLN n
1 192 PHE n
1 193 ALA n
1 194 ILE n
1 195 GLU n
1 196 LEU n
1 197 LYS n
1 198 ASP n
1 199 ASP n
1 200 TRP n
1 201 LEU n
1 202 LYS n
1 203 GLY n
1 204 ARG n
1 205 SER n
1 206 PHE n
1 207 GLN n
1 208 TYR n
1 209 GLY n
1 210 ALA n
1 211 GLU n
1 212 GLY n
1 213 TYR n
1 214 ILE n
1 215 LYS n
1 216 MET n
1 217 SER n
1 218 PRO n
1 219 GLY n
1 220 HIS n
1 221 TRP n
1 222 TYR n
1 223 PHE n
1 224 PRO n
1 225 SER n
1 226 PRO n
1 227 LEU n
#
_entity_src_gen.entity_id 1
_entity_src_gen.gene_src_common_name 'Salmonella typhimurium'
_entity_src_gen.gene_src_genus ?
_entity_src_gen.pdbx_gene_src_gene 'prgH, STM2874'
_entity_src_gen.gene_src_species ?
_entity_src_gen.gene_src_strain ?
_entity_src_gen.gene_src_tissue ?
_entity_src_gen.gene_src_tissue_fraction ?
_entity_src_gen.gene_src_details ?
_entity_src_gen.pdbx_gene_src_fragment ?
_entity_src_gen.pdbx_gene_src_scientific_name 'Salmonella enterica subsp. enterica serovar Typhimurium'
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 90371
_entity_src_gen.pdbx_gene_src_variant ?
_entity_src_gen.pdbx_gene_src_cell_line ?
_entity_src_gen.pdbx_gene_src_atcc ?
_entity_src_gen.pdbx_gene_src_organ ?
_entity_src_gen.pdbx_gene_src_organelle ?
_entity_src_gen.pdbx_gene_src_cell ?
_entity_src_gen.pdbx_gene_src_cellular_location ?
_entity_src_gen.host_org_common_name ?
_entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli'
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008
_entity_src_gen.host_org_genus ?
_entity_src_gen.pdbx_host_org_gene ?
_entity_src_gen.pdbx_host_org_organ ?
_entity_src_gen.host_org_species ?
_entity_src_gen.pdbx_host_org_tissue ?
_entity_src_gen.pdbx_host_org_tissue_fraction ?
_entity_src_gen.pdbx_host_org_strain 'BL21(DE3)'
_entity_src_gen.pdbx_host_org_variant ?
_entity_src_gen.pdbx_host_org_cell_line ?
_entity_src_gen.pdbx_host_org_atcc ?
_entity_src_gen.pdbx_host_org_culture_collection ?
_entity_src_gen.pdbx_host_org_cell ?
_entity_src_gen.pdbx_host_org_organelle ?
_entity_src_gen.pdbx_host_org_cellular_location ?
_entity_src_gen.pdbx_host_org_vector_type ?
_entity_src_gen.pdbx_host_org_vector ?
_entity_src_gen.plasmid_name ?
_entity_src_gen.plasmid_details ?
_entity_src_gen.pdbx_description ?
#
_struct_ref.id 1
_struct_ref.db_name UNP
_struct_ref.db_code PRGH_SALTY
_struct_ref.pdbx_db_accession P41783
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code
;AAELDSLLGQEKERFQVLPGRDKMLYVAAQNERDTLWARQVLARGDYDKNARVINENEEN
KRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSV
NITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRT
WGGRYVQFAIELKDDWLKGRSFQYGAEGYIKMSPGHWYFPSPL
;
_struct_ref.pdbx_align_begin 170
_struct_ref.biol_id .
#
loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 4G1I A 5 ? 227 ? P41783 170 392 170 392
2 1 4G1I B 5 ? 227 ? P41783 170 392 170 392
#
loop_
_struct_ref_seq_dif.align_id
_struct_ref_seq_dif.pdbx_pdb_id_code
_struct_ref_seq_dif.mon_id
_struct_ref_seq_dif.pdbx_pdb_strand_id
_struct_ref_seq_dif.seq_num
_struct_ref_seq_dif.pdbx_pdb_ins_code
_struct_ref_seq_dif.pdbx_seq_db_name
_struct_ref_seq_dif.pdbx_seq_db_accession_code
_struct_ref_seq_dif.db_mon_id
_struct_ref_seq_dif.pdbx_seq_db_seq_num
_struct_ref_seq_dif.details
_struct_ref_seq_dif.pdbx_auth_seq_num
_struct_ref_seq_dif.pdbx_ordinal
1 4G1I GLY A 1 ? UNP P41783 ? ? 'EXPRESSION TAG' 166 1
1 4G1I SER A 2 ? UNP P41783 ? ? 'EXPRESSION TAG' 167 2
1 4G1I HIS A 3 ? UNP P41783 ? ? 'EXPRESSION TAG' 168 3
1 4G1I MET A 4 ? UNP P41783 ? ? 'EXPRESSION TAG' 169 4
2 4G1I GLY B 1 ? UNP P41783 ? ? 'EXPRESSION TAG' 166 5
2 4G1I SER B 2 ? UNP P41783 ? ? 'EXPRESSION TAG' 167 6
2 4G1I HIS B 3 ? UNP P41783 ? ? 'EXPRESSION TAG' 168 7
2 4G1I MET B 4 ? UNP P41783 ? ? 'EXPRESSION TAG' 169 8
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.130
LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.174
ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.104
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
GLY 'PEPTIDE LINKING' y GLYCINE ? 'C2 H5 N O2' 75.067
GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.146
ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.210
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.191
VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.147
PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.132
LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.197
MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.207
TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.191
ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.094
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.119
THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.120
TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.228
ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.174
HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.164
1PE NON-POLYMER . 'PENTAETHYLENE GLYCOL' PEG400 'C10 H22 O6' 238.280
PO4 NON-POLYMER . 'PHOSPHATE ION' ? 'O4 P -3' 94.971
HOH NON-POLYMER . WATER ? 'H2 O' 18.015
#
_exptl.entry_id 4G1I
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 2.02
_exptl_crystal.density_percent_sol 38.97
_exptl_crystal.description ?
_exptl_crystal.F_000 ?
_exptl_crystal.preparation ?
#
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP'
_exptl_crystal_grow.temp 293
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pH 8.5
_exptl_crystal_grow.pdbx_pH_range ?
_exptl_crystal_grow.pdbx_details '100 mM Bicine, pH 8.5, 20% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K'
#
_diffrn.id 1
_diffrn.ambient_temp 93
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
#
_diffrn_detector.diffrn_id 1
_diffrn_detector.detector CCD
_diffrn_detector.type 'RAYONIX MX300HE'
_diffrn_detector.pdbx_collection_date 2011-05
_diffrn_detector.details ?
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.monochromator 'double crystal Si(111)'
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 0.97949
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source SYNCHROTRON
_diffrn_source.type 'CLSI BEAMLINE 08ID-1'
_diffrn_source.pdbx_synchrotron_site CLSI
_diffrn_source.pdbx_synchrotron_beamline 08ID-1
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 0.97949
#
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
_reflns.entry_id 4G1I
_reflns.observed_criterion_sigma_I ?
_reflns.observed_criterion_sigma_F ?
_reflns.d_resolution_low 50
_reflns.d_resolution_high 1.75
_reflns.number_obs 43189
_reflns.number_all ?
_reflns.percent_possible_obs 99.5
_reflns.pdbx_Rmerge_I_obs 0.048
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI 14.9
_reflns.B_iso_Wilson_estimate ?
_reflns.pdbx_redundancy 3.7
_reflns.R_free_details ?
_reflns.limit_h_max ?
_reflns.limit_h_min ?
_reflns.limit_k_max ?
_reflns.limit_k_min ?
_reflns.limit_l_max ?
_reflns.limit_l_min ?
_reflns.observed_criterion_F_max ?
_reflns.observed_criterion_F_min ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
#
_reflns_shell.pdbx_diffrn_id 1
_reflns_shell.pdbx_ordinal 1
_reflns_shell.d_res_high 1.75
_reflns_shell.d_res_low 1.84
_reflns_shell.percent_possible_all 99.9
_reflns_shell.Rmerge_I_obs 0.495
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.meanI_over_sigI_obs 2.8
_reflns_shell.pdbx_redundancy 3.7
_reflns_shell.percent_possible_obs ?
_reflns_shell.number_unique_all ?
_reflns_shell.number_measured_all ?
_reflns_shell.number_measured_obs ?
_reflns_shell.number_unique_obs ?
_reflns_shell.pdbx_chi_squared ?
#
_computing.entry_id 4G1I
_computing.pdbx_data_reduction_ii HKL-2000
_computing.pdbx_data_reduction_ds SCALEPACK
_computing.data_collection MxDC
_computing.structure_solution AutoMR
_computing.structure_refinement 'PHENIX (phenix.refine: 1.8.1_1168)'
_computing.pdbx_structure_refinement_method ?
#
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.entry_id 4G1I
_refine.pdbx_diffrn_id 1
_refine.pdbx_TLS_residual_ADP_flag ?
_refine.ls_number_reflns_obs 36630
_refine.ls_number_reflns_all ?
_refine.pdbx_ls_sigma_I ?
_refine.pdbx_ls_sigma_F 1.35
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.ls_d_res_low 45.957
_refine.ls_d_res_high 1.850
_refine.ls_percent_reflns_obs 99.33
_refine.ls_R_factor_obs 0.1758
_refine.ls_R_factor_all ?
_refine.ls_R_factor_R_work 0.1736
_refine.ls_R_factor_R_free 0.2139
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_percent_reflns_R_free 5.01
_refine.ls_number_reflns_R_free 1835
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.occupancy_min ?
_refine.occupancy_max ?
_refine.correlation_coeff_Fo_to_Fc ?
_refine.correlation_coeff_Fo_to_Fc_free ?
_refine.B_iso_mean ?
_refine.aniso_B[1][1] 1.7682
_refine.aniso_B[2][2] -7.9600
_refine.aniso_B[3][3] 6.1918
_refine.aniso_B[1][2] -0.0000
_refine.aniso_B[1][3] -5.6761
_refine.aniso_B[2][3] -0.0000
_refine.solvent_model_details 'FLAT BULK SOLVENT MODEL'
_refine.solvent_model_param_ksol ?
_refine.solvent_model_param_bsol ?
_refine.pdbx_solvent_vdw_probe_radii 1.11
_refine.pdbx_solvent_ion_probe_radii ?
_refine.pdbx_solvent_shrinkage_radii 0.90
_refine.pdbx_ls_cross_valid_method ?
_refine.details ?
_refine.pdbx_starting_model 'PDB ENTRY 3GR0'
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_isotropic_thermal_model ?
_refine.pdbx_stereochemistry_target_values ML
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_R_Free_selection_details ?
_refine.pdbx_overall_ESU_R ?
_refine.pdbx_overall_ESU_R_Free ?
_refine.overall_SU_ML 0.22
_refine.pdbx_overall_phase_error 22.57
_refine.overall_SU_B ?
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
_refine.ls_redundancy_reflns_obs ?
_refine.B_iso_min ?
_refine.B_iso_max ?
_refine.overall_SU_R_free ?
_refine.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.overall_FOM_free_R_set ?
_refine.overall_FOM_work_R_set ?
#
_refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 3182
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 76
_refine_hist.number_atoms_solvent 233
_refine_hist.number_atoms_total 3491
_refine_hist.d_res_high 1.850
_refine_hist.d_res_low 45.957
#
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.number
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.pdbx_restraint_function
f_bond_d 0.015 ? ? 3320 'X-RAY DIFFRACTION' ?
f_angle_d 1.545 ? ? 4464 'X-RAY DIFFRACTION' ?
f_dihedral_angle_d 18.006 ? ? 1281 'X-RAY DIFFRACTION' ?
f_chiral_restr 0.118 ? ? 463 'X-RAY DIFFRACTION' ?
f_plane_restr 0.007 ? ? 572 'X-RAY DIFFRACTION' ?
#
loop_
_refine_ls_shell.pdbx_refine_id
_refine_ls_shell.pdbx_total_number_of_bins_used
_refine_ls_shell.d_res_high
_refine_ls_shell.d_res_low
_refine_ls_shell.number_reflns_R_work
_refine_ls_shell.R_factor_R_work
_refine_ls_shell.percent_reflns_obs
_refine_ls_shell.R_factor_R_free
_refine_ls_shell.R_factor_R_free_error
_refine_ls_shell.percent_reflns_R_free
_refine_ls_shell.number_reflns_R_free
_refine_ls_shell.number_reflns_all
_refine_ls_shell.R_factor_all
_refine_ls_shell.redundancy_reflns_obs
_refine_ls_shell.number_reflns_obs
'X-RAY DIFFRACTION' ? 1.8500 1.9000 2656 0.2385 100.00 0.3163 ? ? 130 ? ? ? ?
'X-RAY DIFFRACTION' ? 1.9000 1.9559 2688 0.2081 100.00 0.2653 ? ? 144 ? ? ? ?
'X-RAY DIFFRACTION' ? 1.9559 2.0191 2640 0.1971 100.00 0.2549 ? ? 140 ? ? ? ?
'X-RAY DIFFRACTION' ? 2.0191 2.0912 2670 0.1836 100.00 0.2462 ? ? 140 ? ? ? ?
'X-RAY DIFFRACTION' ? 2.0912 2.1750 2649 0.1799 100.00 0.1970 ? ? 139 ? ? ? ?
'X-RAY DIFFRACTION' ? 2.1750 2.2739 2658 0.1694 100.00 0.2386 ? ? 140 ? ? ? ?
'X-RAY DIFFRACTION' ? 2.2739 2.3938 2683 0.1750 100.00 0.2357 ? ? 135 ? ? ? ?
'X-RAY DIFFRACTION' ? 2.3938 2.5438 2691 0.1614 100.00 0.1967 ? ? 133 ? ? ? ?
'X-RAY DIFFRACTION' ? 2.5438 2.7402 2667 0.1724 100.00 0.2186 ? ? 147 ? ? ? ?
'X-RAY DIFFRACTION' ? 2.7402 3.0159 2688 0.1659 99.00 0.2055 ? ? 144 ? ? ? ?
'X-RAY DIFFRACTION' ? 3.0159 3.4522 2688 0.1669 99.00 0.2066 ? ? 132 ? ? ? ?
'X-RAY DIFFRACTION' ? 3.4522 4.3488 2682 0.1514 99.00 0.1952 ? ? 161 ? ? ? ?
'X-RAY DIFFRACTION' ? 4.3488 45.9714 2735 0.1898 96.00 0.2124 ? ? 150 ? ? ? ?
#
_struct.entry_id 4G1I
_struct.title 'Structure of the PrgH periplasmic domain'
_struct.pdbx_descriptor 'Protein prgH'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 4G1I
_struct_keywords.pdbx_keywords 'CELL INVASION'
_struct_keywords.text 'Ring-building motif, Type III secretion, InvG, CELL INVASION'
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 1 ?
C N N 2 ?
D N N 2 ?
E N N 3 ?
F N N 3 ?
G N N 2 ?
H N N 2 ?
I N N 3 ?
J N N 3 ?
K N N 4 ?
L N N 4 ?
#
_struct_biol.id 1
_struct_biol.details
'Though the cloned protein construct that was crystallized is a monomer, the full-length version of this protein forms a 24-mer.'
#
loop_
_struct_conf.conf_type_id
_struct_conf.id
_struct_conf.pdbx_PDB_helix_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.pdbx_beg_PDB_ins_code
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.pdbx_end_PDB_ins_code
_struct_conf.beg_auth_comp_id
_struct_conf.beg_auth_asym_id
_struct_conf.beg_auth_seq_id
_struct_conf.end_auth_comp_id
_struct_conf.end_auth_asym_id
_struct_conf.end_auth_seq_id
_struct_conf.pdbx_PDB_helix_class
_struct_conf.details
_struct_conf.pdbx_PDB_helix_length
HELX_P HELX_P1 1 GLU A 7 ? GLN A 14 ? GLU A 172 GLN A 179 1 ? 8
HELX_P HELX_P2 2 ASN A 35 ? ARG A 48 ? ASN A 200 ARG A 213 1 ? 14
HELX_P HELX_P3 3 ASN A 59 ? TYR A 75 ? ASN A 224 TYR A 240 1 ? 17
HELX_P HELX_P4 4 SER A 103 ? MET A 118 ? SER A 268 MET A 283 1 ? 16
HELX_P HELX_P5 5 ASP A 130 ? GLN A 145 ? ASP A 295 GLN A 310 1 ? 16
HELX_P HELX_P6 6 ASP A 167 ? GLY A 186 ? ASP A 332 GLY A 351 1 ? 20
HELX_P HELX_P7 7 LEU B 8 ? GLN B 14 ? LEU B 173 GLN B 179 1 ? 7
HELX_P HELX_P8 8 ASN B 35 ? GLY B 49 ? ASN B 200 GLY B 214 1 ? 15
HELX_P HELX_P9 9 ASN B 59 ? TYR B 75 ? ASN B 224 TYR B 240 1 ? 17
HELX_P HELX_P10 10 SER B 103 ? MET B 118 ? SER B 268 MET B 283 1 ? 16
HELX_P HELX_P11 11 ASP B 130 ? GLN B 145 ? ASP B 295 GLN B 310 1 ? 16
HELX_P HELX_P12 12 ASP B 167 ? GLY B 186 ? ASP B 332 GLY B 351 1 ? 20
#
_struct_conf_type.id HELX_P
_struct_conf_type.criteria ?
_struct_conf_type.reference ?
#
loop_
_struct_sheet.id
_struct_sheet.type
_struct_sheet.number_strands
_struct_sheet.details
A ? 3 ?
B ? 3 ?
C ? 3 ?
D ? 3 ?
E ? 3 ?
F ? 3 ?
#
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
A 1 2 ? anti-parallel
A 2 3 ? parallel
B 1 2 ? anti-parallel
B 2 3 ? parallel
C 1 2 ? anti-parallel
C 2 3 ? parallel
D 1 2 ? anti-parallel
D 2 3 ? parallel
E 1 2 ? anti-parallel
E 2 3 ? parallel
F 1 2 ? anti-parallel
F 2 3 ? parallel
#
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.pdbx_beg_PDB_ins_code
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.pdbx_end_PDB_ins_code
_struct_sheet_range.symmetry
_struct_sheet_range.beg_auth_comp_id
_struct_sheet_range.beg_auth_asym_id
_struct_sheet_range.beg_auth_seq_id
_struct_sheet_range.end_auth_comp_id
_struct_sheet_range.end_auth_asym_id
_struct_sheet_range.end_auth_seq_id
A 1 PHE A 19 ? PRO A 23 ? ? PHE A 184 PRO A 188
A 2 LEU A 29 ? ALA A 33 ? ? LEU A 194 ALA A 198
A 3 ALA A 55 ? ILE A 58 ? ? ALA A 220 ILE A 223
B 1 TYR A 80 ? HIS A 84 ? ? TYR A 245 HIS A 249
B 2 VAL A 92 ? SER A 96 ? ? VAL A 257 SER A 261
B 3 ASN A 125 ? MET A 129 ? ? ASN A 290 MET A 294
C 1 TYR A 149 ? HIS A 154 ? ? TYR A 314 HIS A 319
C 2 GLY A 157 ? GLY A 164 ? ? GLY A 322 GLY A 329
C 3 VAL A 190 ? LEU A 196 ? ? VAL A 355 LEU A 361
D 1 GLN B 20 ? PRO B 23 ? ? GLN B 185 PRO B 188
D 2 LEU B 29 ? ALA B 32 ? ? LEU B 194 ALA B 197
D 3 ALA B 55 ? ILE B 58 ? ? ALA B 220 ILE B 223
E 1 TYR B 80 ? HIS B 84 ? ? TYR B 245 HIS B 249
E 2 VAL B 92 ? SER B 96 ? ? VAL B 257 SER B 261
E 3 ASN B 125 ? MET B 129 ? ? ASN B 290 MET B 294
F 1 TYR B 149 ? ASN B 153 ? ? TYR B 314 ASN B 318
F 2 VAL B 158 ? ILE B 162 ? ? VAL B 323 ILE B 327
F 3 VAL B 190 ? ILE B 194 ? ? VAL B 355 ILE B 359
#
loop_
_pdbx_struct_sheet_hbond.sheet_id
_pdbx_struct_sheet_hbond.range_id_1
_pdbx_struct_sheet_hbond.range_id_2
_pdbx_struct_sheet_hbond.range_1_label_atom_id
_pdbx_struct_sheet_hbond.range_1_label_comp_id
_pdbx_struct_sheet_hbond.range_1_label_asym_id
_pdbx_struct_sheet_hbond.range_1_label_seq_id
_pdbx_struct_sheet_hbond.range_1_PDB_ins_code
_pdbx_struct_sheet_hbond.range_1_auth_atom_id
_pdbx_struct_sheet_hbond.range_1_auth_comp_id
_pdbx_struct_sheet_hbond.range_1_auth_asym_id
_pdbx_struct_sheet_hbond.range_1_auth_seq_id
_pdbx_struct_sheet_hbond.range_2_label_atom_id
_pdbx_struct_sheet_hbond.range_2_label_comp_id
_pdbx_struct_sheet_hbond.range_2_label_asym_id
_pdbx_struct_sheet_hbond.range_2_label_seq_id
_pdbx_struct_sheet_hbond.range_2_PDB_ins_code
_pdbx_struct_sheet_hbond.range_2_auth_atom_id
_pdbx_struct_sheet_hbond.range_2_auth_comp_id
_pdbx_struct_sheet_hbond.range_2_auth_asym_id
_pdbx_struct_sheet_hbond.range_2_auth_seq_id
A 1 2 N LEU A 22 ? N LEU A 187 O TYR A 30 ? O TYR A 195
A 2 3 N VAL A 31 ? N VAL A 196 O ILE A 58 ? O ILE A 223
B 1 2 N HIS A 84 ? N HIS A 249 O VAL A 92 ? O VAL A 257
B 2 3 N LEU A 95 ? N LEU A 260 O MET A 129 ? O MET A 294
C 1 2 N SER A 150 ? N SER A 315 O VAL A 161 ? O VAL A 326
C 2 3 N ILE A 162 ? N ILE A 327 O GLU A 195 ? O GLU A 360
D 1 2 N LEU B 22 ? N LEU B 187 O TYR B 30 ? O TYR B 195
D 2 3 N VAL B 31 ? N VAL B 196 O ARG B 56 ? O ARG B 221
E 1 2 N HIS B 84 ? N HIS B 249 O VAL B 92 ? O VAL B 257
E 2 3 N LEU B 95 ? N LEU B 260 O MET B 129 ? O MET B 294
F 1 2 N SER B 150 ? N SER B 315 O VAL B 161 ? O VAL B 326
F 2 3 N ILE B 162 ? N ILE B 327 O ALA B 193 ? O ALA B 358
#
loop_
_struct_site.id
_struct_site.details
_struct_site.pdbx_evidence_code
AC1 'BINDING SITE FOR RESIDUE 1PE A 401' SOFTWARE
AC2 'BINDING SITE FOR RESIDUE 1PE A 402' SOFTWARE
AC3 'BINDING SITE FOR RESIDUE PO4 A 403' SOFTWARE
AC4 'BINDING SITE FOR RESIDUE PO4 A 404' SOFTWARE
AC5 'BINDING SITE FOR RESIDUE 1PE B 401' SOFTWARE
AC6 'BINDING SITE FOR RESIDUE 1PE B 402' SOFTWARE
AC7 'BINDING SITE FOR RESIDUE PO4 B 403' SOFTWARE
AC8 'BINDING SITE FOR RESIDUE PO4 B 404' SOFTWARE
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 8 TYR A 74 ? TYR A 239 . . 1_555 ?
2 AC1 8 TYR A 75 ? TYR A 240 . . 1_555 ?
3 AC1 8 GLN A 98 ? GLN A 263 . . 4_445 ?
4 AC1 8 ASN A 100 ? ASN A 265 . . 4_445 ?
5 AC1 8 THR A 101 ? THR A 266 . . 4_445 ?
6 AC1 8 VAL A 109 ? VAL A 274 . . 1_555 ?
7 AC1 8 LYS A 113 ? LYS A 278 . . 1_555 ?
8 AC1 8 HOH K . ? HOH A 614 . . 1_555 ?
9 AC2 8 GLU A 62 ? GLU A 227 . . 1_555 ?
10 AC2 8 ARG A 66 ? ARG A 231 . . 1_555 ?
11 AC2 8 LEU A 117 ? LEU A 282 . . 1_555 ?
12 AC2 8 THR A 133 ? THR A 298 . . 1_545 ?
13 AC2 8 GLY A 136 ? GLY A 301 . . 1_545 ?
14 AC2 8 ALA A 140 ? ALA A 305 . . 1_545 ?
15 AC2 8 HOH K . ? HOH A 505 . . 1_545 ?
16 AC2 8 TRP B 200 ? TRP B 365 . . 1_554 ?
17 AC3 4 THR A 133 ? THR A 298 . . 1_555 ?
18 AC3 4 GLN A 137 ? GLN A 302 . . 1_555 ?
19 AC3 4 TRP A 185 ? TRP A 350 . . 1_555 ?
20 AC3 4 HOH K . ? HOH A 630 . . 1_555 ?
21 AC4 5 MET A 129 ? MET A 294 . . 1_555 ?
22 AC4 5 ASP A 130 ? ASP A 295 . . 1_555 ?
23 AC4 5 THR A 133 ? THR A 298 . . 1_555 ?
24 AC4 5 HOH K . ? HOH A 571 . . 1_555 ?
25 AC4 5 HOH K . ? HOH A 630 . . 1_555 ?
26 AC5 3 TYR B 74 ? TYR B 239 . . 1_555 ?
27 AC5 3 LYS B 113 ? LYS B 278 . . 1_555 ?
28 AC5 3 ALA B 116 ? ALA B 281 . . 1_555 ?
29 AC6 7 ARG B 56 ? ARG B 221 . . 1_555 ?
30 AC6 7 ARG B 66 ? ARG B 231 . . 1_555 ?
31 AC6 7 LEU B 117 ? LEU B 282 . . 1_555 ?
32 AC6 7 THR B 133 ? THR B 298 . . 1_565 ?
33 AC6 7 GLY B 136 ? GLY B 301 . . 1_565 ?
34 AC6 7 GLN B 137 ? GLN B 302 . . 1_565 ?
35 AC6 7 HOH L . ? HOH B 584 . . 1_555 ?
36 AC7 7 GLY A 164 ? GLY A 329 . . 1_556 ?
37 AC7 7 ALA A 165 ? ALA A 330 . . 1_556 ?
38 AC7 7 LEU A 166 ? LEU A 331 . . 1_556 ?
39 AC7 7 LYS A 197 ? LYS A 362 . . 1_556 ?
40 AC7 7 ARG B 175 ? ARG B 340 . . 1_555 ?
41 AC7 7 VAL B 178 ? VAL B 343 . . 1_555 ?
42 AC7 7 ASP B 179 ? ASP B 344 . . 1_555 ?
43 AC8 4 ALA A 193 ? ALA A 358 . . 1_556 ?
44 AC8 4 HOH K . ? HOH A 581 . . 1_556 ?
45 AC8 4 ARG B 152 ? ARG B 317 . . 1_555 ?
46 AC8 4 HOH L . ? HOH B 569 . . 1_555 ?
#
_database_PDB_matrix.entry_id 4G1I
_database_PDB_matrix.origx[1][1] 1.000000
_database_PDB_matrix.origx[1][2] 0.000000
_database_PDB_matrix.origx[1][3] 0.000000
_database_PDB_matrix.origx[2][1] 0.000000
_database_PDB_matrix.origx[2][2] 1.000000
_database_PDB_matrix.origx[2][3] 0.000000
_database_PDB_matrix.origx[3][1] 0.000000
_database_PDB_matrix.origx[3][2] 0.000000
_database_PDB_matrix.origx[3][3] 1.000000
_database_PDB_matrix.origx_vector[1] 0.00000
_database_PDB_matrix.origx_vector[2] 0.00000
_database_PDB_matrix.origx_vector[3] 0.00000
#
_atom_sites.entry_id 4G1I
_atom_sites.Cartn_transform_axes ?
_atom_sites.fract_transf_matrix[1][1] 0.003788
_atom_sites.fract_transf_matrix[1][2] 0.000000