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Crystallization Contaminants

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Marcin Wojdyr edited this page Sep 28, 2016 · 33 revisions

A list of crystallization contaminants deposited in PDB that we (plan to) use for quick screening.

The initial version of the list is taken from Table 1 of E. Niedzialkowska et al., Protein Science, 25, 720 (2016). We are grateful to the authors for compiling the neat table. Previously, the usually referred to resource was this summary from ccp4bb (2010). Currently, the ContaMiner project, announced in 2016, maintains much longer list of contaminants, but focusing on unique domains (as appropriate for MR), not unique unit cells.

Like in the original paper, PDB IDs should be selected to represent distinct conformational states of the given protein.

UniProtKB entry names are useful for cross-checking with the ContaMiner list. In some cases the name corresponds to only one of the chains in the crystal, or to a homolog.

Do you see something missing from the list below? Feel free to edit it (you should see the [Edit] button when logged to GitHub) or email wojdyr@gmail.com.

Affinity, solubility, anti-aggregation tags

  • MALE_ECOLI Maltose-binding protein (MBP) - 1LLS, 1MPB, 3PUW, 3SEU, 4KYC
  • MALE_ECO57
  • GST26_SCHJA Glutathione-S-transferase (GST) - 4ECB
  • THIO_ECOLI Thioredoxin (Trx) - 1F6M, 2AJQ, 2H73, 4HU9, 4X43
  • NUSA_ECOLI N-Utilization substance (NusA) - 1U9L, 1WCN, 2KWP, 4MTN
  • NUSG_ECOLI
  • SUMO1_HUMAN Small ubiquitin related modifier 1 (SUMO1) - 2UYZ, 1Z5S, 4WJQ, 2IO2
  • DHAA_RHORH Haloalkane dehalogenase - 4E46
  • BCCP_ECOLI

Proteases and exogenous proteins added during purification or crystallization

  • POLG_TEV Tobacco etch virus (TEV) - 1LVM
  • POLG_HRV2 Rhinovirus 3C protease - 1CQQ
  • POLG_HRV14
  • ULP1_YEAST SUMO protease C-terminal domain - 2HL9
  • ENTK_BOVIN Enterokinase - 1EKB
  • TRY1_BOVIN Trypsin - 3UY9
  • CTRA_BOVIN Chymotrypsin - 1GGD
  • THRB_HUMAN Thrombin (active form) - 3SQE, 1MH0, 4H6T
  • THRB_BOVIN
  • THER_BACTH Thermolysin - 4D9W
  • PRTK_ENGAL Proteinase K - 3DVS
  • PEPA_PIG Pepsin - 5PEP
  • ELNE_HUMAN Neutrophil elastase - 5ABW
  • PLMP_GRIFR LysN Peptidyl-Lys metalloendopeptidase - 1GE7
  • LYSC_LYSEN Lysyl endopeptidase - 4NSY
  • FA10_BOVIN Factor Xa - 1KIG
  • FA10_HUMAN
  • LYSC_CHICK Lysozyme - 4TWS, 4PRQ, 1AKI
  • DNAS1_BOVIN DNase protein - 2A40, 2A41, 2A42, 3W3D

Host proteins

  • ZINT_ECOLI Metal-binding lipocalin (YodA) - 1OEJ, 4TNN
  • CAN_ECOLI Carbonic anhydrase (YadF) - 2ESF
  • FUR_ECOLI Ferric uptake regulator (Fur) - 2FU4
  • CRP_ECOLI cAMP-regulatory protein (CRP) - 1CGP, 2CGP, 2GZW, 3FWE, 3HIF, 3N4M, 3QOP, 4FT8, 4HZF, 4I0A, 4I0B, 4N9H, 4N9I
  • GLMS_ECOLI Glucosamine-6-phosphate synthase (GlmS) - 4AMV, 1JXA, 3OOJ, 2J6H
  • GLGA_ECOLI Glycogen synthase (GlgA) - 2QZS
  • ODO1_ECOLI Component 1 of the 2-oxoglutarate dehydrogenase complex (ODO1) - 2JGD
  • ODO2_ECOLI Component E2 of dihydrolipoamide succinyltransferase (ODO2) - 1C4T
  • ARNA_ECOLI Formyl transferase (YfbG, ArnA) - 1U9J, 1YRW, 1Z7E, 2BLN, 4WKG
  • SODC_ECOLI Cu/Zn-superoxide dismutase (Cu/Zn-SODM) - 1ESO
  • CAT_ECOLX Chloramphenicol-O-acetyl transferase (CAT) - 1Q23
  • HFQ_ECOLI Host factor-I protein (Hfq) - 3VU3, 4RCB
  • CATE_ECOLI
  • OMPF_ECOLI Porin (OmpF) -
  • CH60_ECOLI GroEL Chaperonin (GROEL) - 1SS8, 1SVT, 1SX3
  • IPYR_ECOLI
  • TKT1_ECOLI
  • KDSA_ECOLI
  • SLYD_ECOLI
  • DHSC_ECOLI
  • ACRB_ECOLI
  • KPYK1_ECOLI
  • SYK2_ECOLI
  • SYA_ECOLI
  • KATG_ECOLI
  • BFR_ECOLI
  • DEGS_ECOLI
  • TPIS_ECOLI
  • GATD_ECOLI
  • ARCA_ECOLI
  • LACI_ECOLI
  • RS15_ECOLI
  • AGAL_ECOLI
  • G6PD_ECOLI
  • ARGE_ECOLI
  • OMPF_ECOLI
  • ADH1_YEAST
  • PNC1_YEAST
  • _STRM5 Phosphate-Binding Protein from Stenotrophomonas maltophilia - 5JK4
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