- PDB-4weq: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -
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Open data
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Basic information
Entry
Database: PDB / ID: 4weq
Title
Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADP and sulfate
Components
NAD-dependent dehydrogenase
Keywords
OXIDOREDUCTASE / NADP-dependent dehydrogenase / Structural Genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Mass: 37264.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The protein was subjected to limited proteolysis by chymotrypsin right before crystallization. Supposingly the HIS-tag was cleaved Source: (gene. exp.) Rhizobium meliloti (bacteria) / Strain: 1021 / Gene: R00152, SMc02828, CAC41539.1 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q92T34, glyoxylate reductase (NADP+)
Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.92 Å3/Da / Density % sol: 68.65 %
Crystal grow
Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, and 5 mM NADP were mixed with 0.2 ul of the MCSG-I condition #6 (0.2 M Ammonium ...Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, and 5 mM NADP were mixed with 0.2 ul of the MCSG-I condition #6 (0.2 M Ammonium Sulfate 0.1 M Bis-Tris:HCl pH 5.5 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization, the protein-ligand mixture was incubated with 1/40 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours PH range: 5.5-7.5
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1886 / WRfactor Rwork: 0.1534 / FOM work R set: 0.8698 / SU B: 5.645 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1059 / SU Rfree: 0.1117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.112 / SU Rfree Cruickshank DPI: 0.1117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1962
1769
4.8 %
RANDOM
Rwork
0.1543
35220
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obs
0.1561
35220
99.92 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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