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- PDB-4pvd: Crystal structure of yeast methylglyoxal/isovaleraldehyde reducta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pvd | ||||||
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Title | Crystal structure of yeast methylglyoxal/isovaleraldehyde reductase Gre2 complexed with NADPH | ||||||
![]() | NADPH-dependent methylglyoxal reductase GRE2 | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / Reductase / NADPH binding | ||||||
Function / homology | ![]() 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 / 3-beta-hydroxy-delta5-steroid dehydrogenase (NAD+) activity / filamentous growth / steroid biosynthetic process ...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 / 3-beta-hydroxy-delta5-steroid dehydrogenase (NAD+) activity / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, P.C. / Bao, Z.Z. / Li, W.F. / Zhou, C.Z. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 438 KB | Display | ![]() |
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PDB format | ![]() | 353.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pvcSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38220.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: s288c / Gene: GRE2, YOL151W / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: Q12068, methylglyoxal reductase (NADPH), 3-methylbutanal reductase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.41 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 67436 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 15.934 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.515 / Num. unique all: 3332 / Rsym value: 0.463 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PVC Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / SU B: 19.382 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.287 / 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: 50.933 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 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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