Crystallization Contaminants

Marcin Wojdyr edited this page Oct 12, 2018 · 33 revisions

A list of crystallization contaminants deposited in PDB that we use for quick screening. It is derived from the ContaBase, which is maintained at StruBE as a part of the ContaMiner project.

Initially, our list was based on:

Both ① and ② were were published in 2016. Before that the usually referred to resource was this summary from ccp4bb (2010). As of 2018 ② is actively maintained and is a superset of ①.

Contaminer focuses on protein domains for molecular replacement. In Dimple we only do quick screening based on the unit cell parameters.

Items in the list below are each from a different UniRef100 cluster and have:

  • UniProt name LIKE_THIS,
  • description - usually from ① (may refer to a specific domain) or from UniProt
  • PDB IDs - only entries deposited as contaminants (usually co-purified).

We process this page automatically, reading each UniProtKB entry name*:
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.

  • MALE_ECOLI ①② Maltose-binding protein (MBP)
  • GST26_SCHJA ①② Glutathione-S-transferase (GST)
  • THIO_ECOLI ①② Thioredoxin (Trx)
  • NUSA_ECOLI ①② N-Utilization substance (NusA)
  • NUSG_ECOLI ② Transcription termination/antitermination protein
  • SUMO1_HUMAN ①② Small ubiquitin related modifier 1 (SUMO1)
  • DHAA_RHORH ①② Haloalkane dehalogenase
  • BCCP_ECOLI ② Biotin carboxyl carrier protein BCCP
  • POLG_TEV ①② Tobacco etch virus (TEV)
  • POLG_HRV2 ① Rhinovirus 3C protease (in polyprotein)
  • POLG_HRV14 ② Rhinovirus genome polyprotein
  • ULP1_YEAST ①② SUMO protease C-terminal domain
  • ENTK_BOVIN ①② Enterokinase
  • TRY1_BOVIN ①② Trypsin
  • CTRA_BOVIN ①② Chymotrypsin
  • THRB_HUMAN ① Thrombin active form (Prothrombin)
  • THRB_BOVIN ② Prothrombin
  • THER_BACTH ①② Thermolysin
  • PRTK_PARAQ ①② Proteinase K
  • PEPA_PIG ①② Pepsin
  • ELNE_HUMAN ①② Neutrophil elastase
  • PLMP_GRIFR ①② LysN Peptidyl-Lys metalloendopeptidase
  • LYSC_LYSEN ①② Lysyl endopeptidase
  • FA10_BOVIN ① Factor Xa (Coagulation factor X)
  • FA10_HUMAN ② Factor Xa (Coagulation factor X)
  • LYSC_CHICK ①② Lysozyme
  • DNAS1_BOVIN ①② DNase protein
  • ZINT_ECOLI ①② Metal-binding lipocalin (YodA) - 4TNN
  • CAN_ECOLI ①② Carbonic anhydrase (YadF) - 4ZNZ
  • FUR_ECOLI ①② Ferric uptake regulator (Fur)
  • CRP_ECOLI ①② cAMP-regulatory protein (CRP)
  • GLMS_ECOLI ①② Glucosamine-6-phosphate synthase (GlmS)
  • GLGA_ECOLI ①② Glycogen synthase (GlgA)
  • ODO1_ECOLI ①② Component 1 of the 2-oxoglutarate dehydrogenase complex (ODO1)
  • ODO2_ECOLI ①② Component E2 of dihydrolipoamide succinyltransferase (ODO2)
  • ARNA_ECOLI ①② Formyl transferase (YfbG, ArnA)
  • SODC_ECOLI ①② Cu/Zn-superoxide dismutase (Cu/Zn-SODM)
  • CAT_ECOLX ①② Chloramphenicol-O-acetyl transferase (CAT)
  • HFQ_ECOLI ①② Host factor-I protein (Hfq)
  • CATE_ECOLI ② Catalase HPII
  • OMPF_ECOLI ② Porin (OmpF)
  • CH60_ECOLI ② GroEL Chaperonin (GROEL)
  • IPYR_ECOLI ② Inorganic pyrophosphatase
  • TKT1_ECOLI ② Transketolase 1
  • KDSA_ECOLI ② 2-dehydro-3-deoxyphosphooctonate aldolase
  • SLYD_ECOLI ② PPIase
  • DHSC_ECOLI ② Cytochrome b-556
  • ACRB_ECOLI ② Multidrug efflux pump subunit AcrB
  • KPYK1_ECOLI ② Pyruvate kinase I
  • SYK2_ECOLI ② Lysine-tRNA ligase
  • SYA_ECOLI ② Alanine-tRNA ligase
  • KATG_ECOLI ② Catalase-peroxidase
  • BFR_ECOLI ② Bacterioferritin
  • DEGS_ECOLI ② Serine endoprotease DegS
  • TPIS_ECOLI ② Triosephosphate isomerase (tpiA) - 4IOT
  • GATD_ECOLI ② Galactitol-1-phosphate 5-dehydrogenase
  • ARCA_ECOLI ② Aerobic respiration control protein ArcA
  • LACI_ECOLI ② Lactose operon repressor
  • RS15_ECOLI ② 30S ribosomal protein S15
  • AGAL_ECOLI ② Alpha-galactosidase
  • G6PD_ECOLI ② Glucose-6-phosphate 1-dehydrogenase
  • ARGE_ECOLI ② Acetylornithine deacetylase
  • ADH1_YEAST ② Alcohol dehydrogenase 1
  • PNC1_YEAST ② Nicotinamidase
  • B4SL31_STRM5 ② Alkaline phosphatase - 5JK4
  • Q9I4D6_PSEAE probable cysteine hydrolase (YcaC) - 4WGF, 4WH0
  • YCAC_ECOLI ② Probable hydrolase YcaC
  • PHBP_UNKP Phosphate-binding protein, DING family (HPBP) - 2V3Q, 3W9W
  • P83696_ALCXX Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) - 1OBF
  • G3P1_ECOLI ② Glyceraldehyde-3-phosphate dehydrogenase A
  • IDH_ECOLI ② Isocitrate dehydrogenase (NADP)
  • CYNS_SERP5 ② Cyanate hydratase
  • S0AKJ8_SERPL ② Glycerol dehydrogenase DhaD - 4MCA
  • DPS_ECOLI ② DNA protection during starvation protein
  • NAGB_ECOLI ② Glucosamine-6-phosphate deaminase
  • A0A140N6S1_ECOBD ② Gab protein - 2R6S

Do you see a protein missing in the list below? Contact ② – we automatically check that list. If you would like to improve something specific to Dimple: open a new issue.

Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.