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Yorodumi- PDB-4pvc: Crystal structure of yeast methylglyoxal/ isovaleraldehyde reduct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pvc | ||||||
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Title | Crystal structure of yeast methylglyoxal/ isovaleraldehyde reductase Gre2 | ||||||
Components | NADPH-dependent methylglyoxal reductase GRE2 | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Reductase / NADPH binding | ||||||
Function / homology | Function and homology information 3-methylbutanal reductase / 3-methylbutanal reductase [NAD(P)H] activity / 3-methylbutanal reductase (NADH) activity / methylglyoxal reductase (NADPH) / methylglyoxal reductase (NADPH) activity / 3-methylbutanal reductase (NADPH) activity / ergosterol metabolic process / filamentous growth / steroid biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ...3-methylbutanal reductase / 3-methylbutanal reductase [NAD(P)H] activity / 3-methylbutanal reductase (NADH) activity / methylglyoxal reductase (NADPH) / methylglyoxal reductase (NADPH) activity / 3-methylbutanal reductase (NADPH) activity / ergosterol metabolic process / filamentous growth / steroid biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Guo, P.C. / Bao, Z.Z. / Li, W.F. / Zhou, C.Z. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Structural insights into the cofactor-assisted substrate recognition of yeast methylglyoxal/isovaleraldehyde reductase Gre2 Authors: Guo, P.C. / Bao, Z.Z. / Ma, X.X. / Xia, Q. / Li, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pvc.cif.gz | 280 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pvc.ent.gz | 229.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pvc_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 4pvc_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 4pvc_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 4pvc_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/4pvc ftp://data.pdbj.org/pub/pdb/validation_reports/pv/4pvc | HTTPS FTP |
-Related structure data
Related structure data | 4pvdC 1y1pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38220.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: s288c / Gene: GRE2, YOL151W / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q12068, methylglyoxal reductase (NADPH), 3-methylbutanal reductase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.24 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25% polyethylene glycol 2000 mmE, 0.2M (NH4)2SO4, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9701 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9701 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 45207 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 18.07 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.323 / Num. unique all: 2208 / Rsym value: 0.207 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y1P Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.703 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.934 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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