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Crystallization Contaminants

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Marcin Wojdyr edited this page Oct 25, 2016 · 33 revisions

A list of crystallization contaminants deposited in PDB that we use for quick screening, based on:

We are grateful to the authors of ① and ② for compiling neat lists. Both were published in 2016. Previously, the usually referred to resource was this summary from ccp4bb (2010). Note that ② is actively maintained (as of Oct 2016) and is a superset of ①.

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 each UniProtKB entry name below and going*:
UniProtKB entry ⇨ UniRef cluster ⇨ PDB entries (via SIFTS) ⇨ filtered ⇨
⇨ distinct unit cells clustered (complete-linkage) by space group and unit cell.

* We also read the PDB IDs below to add them if they are not yet in the SIFTS mapping, and handle other corner cases.

Do you see a protein missing in the list below? Edit it (you should see the [Edit] button when logged to GitHub) or open an issue. Or contact ② – we automatically check that list.

  • MALE_ECOLI ①② Maltose-binding protein (MBP) - 1LLS, 1MPB, 3PUW, 3SEU, 4KYC
  • GST26_SCHJA ①② Glutathione-S-transferase (GST) - 4ECB
  • THIO_ECOLI ①② Thioredoxin (Trx) - 1F6M, 2AJQ, 2H73, 4HU9, 4X43
  • NUSA_ECOLI ①② N-Utilization substance (NusA) - 1U9L, 4MTN
  • NUSG_ECOLI ②
  • SUMO1_HUMAN ①② Small ubiquitin related modifier 1 (SUMO1) - 2UYZ, 1Z5S, 4WJQ, 2IO2
  • DHAA_RHORH ①② Haloalkane dehalogenase - 4E46
  • BCCP_ECOLI ②
  • POLG_TEV ①② Tobacco etch virus (TEV) - 1LVM
  • POLG_HRV2 ① Rhinovirus 3C protease - 1CQQ
  • POLG_HRV14 ②
  • ULP1_YEAST ①② SUMO protease C-terminal domain - 2HL9
  • ENTK_BOVIN ①② Enterokinase - 1EKB
  • TRY1_BOVIN ①② Trypsin - 3UY9
  • CTRA_BOVIN ①② Chymotrypsin - 1GGD
  • THRB_HUMAN ① Thrombin (active form) - 3SQE, 1MH0, 4H6T
  • THRB_BOVIN ②
  • THER_BACTH ①② Thermolysin - 4D9W
  • PRTK_ENGAL ①② Proteinase K - 3DVS
  • PEPA_PIG ①② Pepsin - 5PEP
  • ELNE_HUMAN ①② Neutrophil elastase - 5ABW
  • PLMP_GRIFR ①② LysN Peptidyl-Lys metalloendopeptidase - 1GE7
  • LYSC_LYSEN ①② Lysyl endopeptidase - 4NSY
  • FA10_BOVIN ① Factor Xa - 1KIG
  • FA10_HUMAN ②
  • LYSC_CHICK ①② Lysozyme - 4TWS, 4PRQ, 1AKI
  • DNAS1_BOVIN ①② DNase protein - 2A40, 2A41, 2A42, 3W3D
  • ZINT_ECOLI ①② Metal-binding lipocalin (YodA) - 1OEJ, 4TNN
  • CAN_ECOLI ①② Carbonic anhydrase (YadF) - 2ESF
  • FUR_ECOLI ①② Ferric uptake regulator (Fur) - 2FU4
  • CRP_ECOLI ①② cAMP-regulatory protein (CRP) - 1CGP, 2CGP, 2GZW, 3FWE, 3HIF, 3N4M, 3QOP, 4FT8, 4HZF, 4I0A, 4I0B, 4N9H, 4N9I
  • GLMS_ECOLI ①② Glucosamine-6-phosphate synthase (GlmS) - 4AMV, 1JXA, 3OOJ, 2J6H
  • GLGA_ECOLI ①② Glycogen synthase (GlgA) - 2QZS
  • ODO1_ECOLI ①② Component 1 of the 2-oxoglutarate dehydrogenase complex (ODO1) - 2JGD
  • ODO2_ECOLI ①② Component E2 of dihydrolipoamide succinyltransferase (ODO2) - 1C4T
  • ARNA_ECOLI ①② Formyl transferase (YfbG, ArnA) - 1U9J, 1YRW, 1Z7E, 2BLN, 4WKG
  • SODC_ECOLI ①② Cu/Zn-superoxide dismutase (Cu/Zn-SODM) - 1ESO
  • CAT_ECOLX ①② Chloramphenicol-O-acetyl transferase (CAT) - 1Q23
  • HFQ_ECOLI ①② Host factor-I protein (Hfq) - 3VU3, 4RCB
  • CATE_ECOLI ②
  • OMPF_ECOLI ② Porin (OmpF) -
  • CH60_ECOLI ② GroEL Chaperonin (GROEL) - 1SS8, 1SVT, 1SX3
  • IPYR_ECOLI ②
  • TKT1_ECOLI ②
  • KDSA_ECOLI ②
  • SLYD_ECOLI ②
  • DHSC_ECOLI ②
  • ACRB_ECOLI ②
  • KPYK1_ECOLI ②
  • SYK2_ECOLI ②
  • SYA_ECOLI ②
  • KATG_ECOLI ②
  • BFR_ECOLI ②
  • DEGS_ECOLI ②
  • TPIS_ECOLI ②
  • GATD_ECOLI ②
  • ARCA_ECOLI ②
  • LACI_ECOLI ②
  • RS15_ECOLI ②
  • AGAL_ECOLI ②
  • G6PD_ECOLI ②
  • ARGE_ECOLI ②
  • ADH1_YEAST ②
  • PNC1_YEAST ②
  • B4SL31_STRM5 ② Alkaline phosphatase - 5JK4
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