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- PDB-4pvc: Crystal structure of yeast methylglyoxal/ isovaleraldehyde reduct... -

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Basic information

Entry
Database: PDB / ID: 4pvc
TitleCrystal structure of yeast methylglyoxal/ isovaleraldehyde reductase Gre2
ComponentsNADPH-dependent methylglyoxal reductase GRE2
KeywordsOXIDOREDUCTASE / Rossmann Fold / Reductase / NADPH binding
Function / homology
Function and homology information


3-methylbutanal reductase / 3-methylbutanal reductase [NAD(P)H] 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
3-beta hydroxysteroid dehydrogenase/isomerase / 3-beta hydroxysteroid dehydrogenase/isomerase family / : / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADPH-dependent methylglyoxal reductase GRE2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuo, P.C. / Bao, Z.Z. / Li, W.F. / Zhou, C.Z.
CitationJournal: 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
DepositionMar 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH-dependent methylglyoxal reductase GRE2
B: NADPH-dependent methylglyoxal reductase GRE2


Theoretical massNumber of molelcules
Total (without water)76,4412
Polymers76,4412
Non-polymers00
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.721, 97.845, 139.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADPH-dependent methylglyoxal reductase GRE2 / 3-methylbutanal reductase / Genes de respuesta a estres protein 2 / Isovaleraldehyde reductase


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 / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9701 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9701 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y1P

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
RfactorNum. reflection% reflectionSelection details
Rfree0.26593 2285 5.1 %RANDOM
Rwork0.22401 ---
obs0.22612 42922 98.77 %-
all-45207 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.934 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å20 Å2
2--0.15 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 0 346 5726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225490
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.9567414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30825.238252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1215986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3691520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214120
X-RAY DIFFRACTIONr_mcbond_it1.1331.53408
X-RAY DIFFRACTIONr_mcangle_it1.90225506
X-RAY DIFFRACTIONr_scbond_it1.42332082
X-RAY DIFFRACTIONr_scangle_it2.4954.51908
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 173 -
Rwork0.269 2883 -
obs--92.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0944-0.0396-0.00850.0708-0.03330.02650.05290.0457-0.06440.0341-0.060.016-0.04640.01950.00710.1068-0.0002-0.01080.1221-0.00060.1172-14.0483-8.619732.2484
20.04770.0319-0.01890.023-0.0090.0392-0.01280.0010.0705-0.01130.020.04860.05570.026-0.00720.1023-0.00770.00070.13110.01090.11252.40310.41561.0368
30.0113-0.0127-0.01640.02080.03660.0838-0.01730.0119-0.02090.0048-0.01050.0143-0.03210.01120.02780.1205-0.0182-0.00240.11540.00730.1131-7.4163-6.987146.9406
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 342
2X-RAY DIFFRACTION2B1 - 342
3X-RAY DIFFRACTION3A401 - 585
4X-RAY DIFFRACTION3B401 - 561

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