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Crystallization Contaminants

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Marcin Wojdyr edited this page Sep 27, 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.

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

UniProtKB entry names are added for easier cross-checking with the ContaMiner list. The name may correspond to only one of chains if the structure is heteromeric.

Anything missing from the list below? Either email wojdyr@gmail.com or edit it yourself. You should see the [Edit] button when logged to GitHub.

Affinity, solubility, anti-aggregation tags

  • MALE_ECOLI Maltose-binding protein (MBP) - 1LLS, 1MPB, 3PUW, 3SEU, 4KYC
  • 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
  • SUMO1_HUMAN Small ubiquitin related modifier 1 (SUMO1) - 2UYZ, 1Z5S, 4WJQ, 2IO2
  • DHAA_RHORH Haloalkane dehalogenase - 4E46

E. coli native 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
  • OMPF_ECOLI Porin (OmpF) -
  • CH60_ECOLI GroEL Chaperonin (GROEL) - 1SS8, 1SVT, 1SX3

Proteases

  • POLG_TEV Tobacco etch virus (TEV) - 1LVM
  • POLG_HRV2 Rhinovirus 3C protease - 1CQQ
  • 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
  • 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

Exogenous proteins

  • LYSC_CHICK Lysozyme - 4TWS, 4PRQ, 1AKI
  • DNAS1_BOVIN DNase protein - 2A40

SIMBAD proteins

  • n/a Phosphate-Binding Protein from Stenotrophomonas maltophilia - 5JK4
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