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Crystallization Contaminants

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Marcin Wojdyr edited this page Oct 12, 2016 · 33 revisions

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

It's mostly based on a list from E. Niedzialkowska et al. and a list from the ContaMiner project.

We are grateful to the authors for compiling neat lists. Previously, the usually referred to resource was this summary from ccp4bb (2010). Both lists focus on protein domains for molecular replacement.

Here, we're also interested in quick screening based on the unit cell parameters. We process this page automatically reading UniProtKB entry names and going:
UniProtKB entry ⇨ UniRef clusters ⇨ a set of PDB entries ⇨ filtering ⇨ clustering (complete-linkage) by space group and unit cell.
(We also read PDB IDs below to handle the case when they are not included in the SIFTS mapping.)
Finally we get this list of distinct unit cells.

Do you see something missing in the list below? Feel free to edit it (you should see the [Edit] button when logged to GitHub). Or email wojdyr@gmail.com. Or contact authors of the two lists above.

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, 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
  • ADH1_YEAST
  • PNC1_YEAST
  • B4SL31_STRM5 Alkaline phosphatase - 5JK4
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