Protein Science (2016) 25(3): 720-33. DOI: 10.1002/pro.2861

Protein purification and crystallization artifacts: the tale usually not told
Ewa Niedzialkowska, Olga Gasiorowska, Katarzyna B. Handing, Karolina A. Majorek, Przemyslaw J. Porebski, Ivan G. Shabalin, Ewelina Zasadzinska, Marcin Cymborowski, Wladek Minor


List of PDB codes that can be used to detect crystallization artifacts using MR

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Name of the protein Molecular weight [kDa] PDB ID Reference
Affinity, solubility, anti-aggregation tags Maltose-binding protein (MBP) 43 1LLS, 1MPB, 3PUW, 3SEU, 4KYC,
Glutathione-S-transferase (GST) 24 4ECB
Thioredoxin (Trx) 11 1F6M, 2AJQ, 2H73, 4HU9, 4X43,
N-Utilization substance (NusA) 55 1U9L[1], 1WCN[2], 2KWP[3], 4MTN[4]
Small ubiquitin related modifier 1 (SUMO1) 12 2UYZ, 1Z5S, 4WJQ, 2IO2
Haloalkane dehalogenase 33 4E46
E. coli native proteins Metal-binding lipocalin (YodA) 25 1OEJ, 4TNN, PMID: 16814929
Carbonic anhydrase (YadF) 25 2ESF PMID: 16814929
Ferric uptake regulator (Fur) 16 2FU4 PMID: 16814929
cAMP-regulatory protein (CRP) 24 1CGP, 2CGP, 2GZW, 3FWE, 3HIF, 3N4M, 3QOP, 4FT8, 4HZF, 4I0A, 4I0B, 4N9H, 4N9I, PMID: 16814929
Glucosamine-6-phosphate synthase (GlmS) 67 4AMV, 1JXA, 3OOJ, 2J6H PMID: 16814929
Glycogen synthase (GlgA) 53 2QZS PMID: 16814929
Component 1 of the 2-oxoglutarate dehydrogenase complex (ODO1) 105 2JGD PMID: 16814929
Component E2 of the dihydrolipoamide succinyltransferase (ODO2) 44 1C4T PMID: 16814929
Formyl transferase (YfbG) 46 1U9J, 1YRW, 1Z7E, 2BLN 4WKG PMID: 16814929
Cu/Zn-superoxide dismutase (Cu/Zn-SODM) 16 1ESO
Chloramphenicol-O-acetyl transferase (CAT) 26 1Q23
Host factor-I protein (Hfq) 11 3VU3 PMID: 27577872
Gab protein 37 1JR7 PMID: 18391407PMID: 27577872
Glycerol dehydrogenase (GlyDH) 39 5XN8 PMID: 28695861
Inorganic pyrophosphatase (PPase) 20 2AUU PMID: 28955968
Proteases Tobacco etch virus (TEV) 28 1LVB, 1LVM
Rhinovirus 3C protease 48 1CQQ, 2XYA
SUMO protease C-terminal domain 26 2HL9
Enterokinase 26 1EKB
Trypsin 26 3UY9
Chymotrypsin 26 1GGD
Thrombin (active form) 36 3SQE, 1MH0, 4H6T
Thermolysin 60 4D9W
Proteinase K 40 3DVS
Pepsin 41 5PEP
Neutrophil elastase 29 5ABW
LysN Peptidyl-Lys metalloendopeptidase 44 1GE7
LysC Lysyl endopeptidase 28 4NSY
Factor Xa 55 1KIG
Exogenous proteins Lysozyme 16 4TWS, 4PRQ, 1AKI

PMC: 3274391

DNase protein 31 2A40

Footnotes

[1] crystal structure of the C-terminal fragment of NusA from E. coli,
[2] NMR structure of the C-terminal fragment of NusA from E. coli,
[3] NMR structure of the N-terminal fragment of NusA from E. coli,
[4] homologous structure from P. limnophilus,

Proteins in italic have been added after the original publication