- PDB-6cia: Crystal structure of aldo-keto reductase from Klebsiella pneumoni... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6cia
Title
Crystal structure of aldo-keto reductase from Klebsiella pneumoniae in complex with NADPH.
Components
Aldo/keto reductase
Keywords
OXIDOREDUCTASE / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information
D-threo-aldose 1-dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor Similarity search - Function
Mass: 31768.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: yhdN_4, yhdN, B1727_06910, B4U21_09420, BN49_2327, CAK82_20800, CQB04_18905, CR230_19100, CTI52_15935, CTI54_15930, PMK1_03573, SAMEA3531778_00013 Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL References: UniProt: W9BFN4, UniProt: A6T7Q7*PLUS, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal grow
Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the Top 96 #90 (0.2 uL 0.1 M Tris: HCl, pH 8.5, 25 % ...Details: 0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the Top 96 #90 (0.2 uL 0.1 M Tris: HCl, pH 8.5, 25 % (w/v) PEG 3350) and 0.1 uL 30%v/v Ethanol (Additive Screen #82) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci)
Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 15.302 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22957
612
5.1 %
RANDOM
Rwork
0.16727
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obs
0.17052
11434
89.94 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å