Crystallization Contaminants
A list of crystallization contaminants deposited in PDB that we use for quick screening, based on:
- ① a list from E. Niedzialkowska et al.,
- ② a list from the ContaMiner project and
- communication with crystallographers.
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.
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
by 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.
It can be visualized as a tree.
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) -
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_ENGAL
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 -
PHBP_UNKP
Phosphate-binding protein, DING family (HPBP) - 2V3Q, 3W9W -
P83696_ALCXX
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) - 1OBF