Crystallization Contaminants

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:

• ① a list from E. Niedzialkowska et al.,
• ② a list from the ContaMiner project and
• communication with crystallographers.

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.