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- PDB-4pvd: Crystal structure of yeast methylglyoxal/isovaleraldehyde reducta... -

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Basic information

Entry
Database: PDB / ID: 4pvd
TitleCrystal structure of yeast methylglyoxal/isovaleraldehyde reductase Gre2 complexed with NADPH
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 / 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
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
Chem-NDP / NADPH-dependent methylglyoxal reductase GRE2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent methylglyoxal reductase GRE2
B: NADPH-dependent methylglyoxal reductase GRE2
C: NADPH-dependent methylglyoxal reductase GRE2
D: NADPH-dependent methylglyoxal reductase GRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,3736
Polymers152,8824
Non-polymers1,4912
Water2,288127
1
A: NADPH-dependent methylglyoxal reductase GRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9662
Polymers38,2201
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH-dependent methylglyoxal reductase GRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9662
Polymers38,2201
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NADPH-dependent methylglyoxal reductase GRE2


Theoretical massNumber of molelcules
Total (without water)38,2201
Polymers38,2201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NADPH-dependent methylglyoxal reductase GRE2


Theoretical massNumber of molelcules
Total (without water)38,2201
Polymers38,2201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.309, 92.891, 201.094
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.: 4
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: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PVC

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
RfactorNum. reflection% reflectionSelection details
Rfree0.28845 3358 5.1 %RANDOM
Rwork0.24235 ---
obs0.24472 63099 99.3 %-
all-67436 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.933 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--3.37 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10193 0 96 127 10416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.007
X-RAY DIFFRACTIONr_angle_refined_deg1.105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.636
X-RAY DIFFRACTIONr_chiral_restr0.082
X-RAY DIFFRACTIONr_gen_planes_refined0.004
X-RAY DIFFRACTIONr_mcbond_it
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 220 -
Rwork0.3 4638 -
obs--99.96 %
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)
11.180.24220.31610.4732-0.15772.1193-0.00340.01640.0062-0.02520.02650.0264-0.0240.3687-0.02310.05140.02920.01680.1083-0.00230.05314.23187.7942111.9829
21.5470.34880.13930.4591-0.6973.43240.09540.0085-0.01710.09970.02060.048-0.37250.1787-0.1160.10080.0260.03330.06370.01460.034914.205653.1748120.7782
32.54981.65532.57933.00430.35963.5059-0.0206-0.1159-0.02080.13460.0030.0061-0.1863-0.1440.01750.10030.06670.01070.1596-0.02650.090915.912549.9042115.0768
40.03950.3926-0.2063.9976-2.09661.09970.0251-0.01460.01710.01490.01980.1402-0.00570.0053-0.04490.07340.06020.03980.2266-0.03270.076315.86594.5718106.1053
50.6718-0.03350.04870.30510.62623.6610.11640.06170.0182-0.0373-0.0464-0.0078-0.0729-0.3283-0.070.03250.01470.00880.04930.020.05227.46977.706664.0518
60.7097-0.0383-0.12160.32990.75044.12240.06930.12480.05570.0009-0.0694-0.00590.0027-0.2570.00010.0408-0.00540.01220.05270.02340.046427.742753.338372.9533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 342
2X-RAY DIFFRACTION2B1 - 342
3X-RAY DIFFRACTION3B401
4X-RAY DIFFRACTION4A401
5X-RAY DIFFRACTION5C1 - 341
6X-RAY DIFFRACTION6D1 - 341

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