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- PDB-8z9f: Crystal structure of glyoxylate reductase from Acetobacter aceti ... -

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Basic information

Entry
Database: PDB / ID: 8z9f
TitleCrystal structure of glyoxylate reductase from Acetobacter aceti in complex with NADH
Components3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / glyoxylate reductase NADH complex form
Function / homology
Function and homology information


organic acid catabolic process / NAD binding / NADP binding / oxidoreductase activity
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMajumder, T.R. / Yoshizawa, T. / Inoue, M. / Aono, R. / Matsumura, H. / Mihara, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2025
Title: Structural insights into the mechanism underlying the dual cofactor specificity of glyoxylate reductase from Acetobacter aceti in the beta-hydroxyacid dehydrogenase family.
Authors: Majumder, T.R. / Yoshizawa, T. / Inoue, M. / Aono, R. / Matsumura, H. / Mihara, H.
History
DepositionApr 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxyisobutyrate dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase
C: 3-hydroxyisobutyrate dehydrogenase
D: 3-hydroxyisobutyrate dehydrogenase
E: 3-hydroxyisobutyrate dehydrogenase
F: 3-hydroxyisobutyrate dehydrogenase
G: 3-hydroxyisobutyrate dehydrogenase
H: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,24613
Polymers263,9198
Non-polymers3,3275
Water19,9431107
1
A: 3-hydroxyisobutyrate dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase
C: 3-hydroxyisobutyrate dehydrogenase
D: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9567
Polymers131,9594
Non-polymers1,9963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17020 Å2
ΔGint-134 kcal/mol
Surface area37800 Å2
MethodPISA
2
E: 3-hydroxyisobutyrate dehydrogenase
F: 3-hydroxyisobutyrate dehydrogenase
G: 3-hydroxyisobutyrate dehydrogenase
H: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2906
Polymers131,9594
Non-polymers1,3312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-124 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.598, 192.500, 118.213
Angle α, β, γ (deg.)90.000, 95.071, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
3-hydroxyisobutyrate dehydrogenase


Mass: 32989.816 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti (bacteria) / Gene: ghr, AAJCM20276_07180 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6S6PLJ6
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.4M MES, 0.2M CaCl2, 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→48.28 Å / Num. obs: 321671 / % possible obs: 95.59 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.41 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1216 / Rpim(I) all: 0.04944 / Net I/σ(I): 17.35
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.181 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 26268 / CC1/2: 0.588 / CC star: 0.861 / Rpim(I) all: 0.5403 / % possible all: 78.46

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.28 Å / SU ML: 0.2145 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 16061 4.99 %
Rwork0.2114 305610 -
obs0.2124 321671 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15731 0 220 1107 17058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006816228
X-RAY DIFFRACTIONf_angle_d0.957522087
X-RAY DIFFRACTIONf_chiral_restr0.05382644
X-RAY DIFFRACTIONf_plane_restr0.00822844
X-RAY DIFFRACTIONf_dihedral_angle_d7.00622348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.38693790.35786890X-RAY DIFFRACTION65.06
1.62-1.630.36734280.34798074X-RAY DIFFRACTION75.59
1.63-1.650.32724750.31389364X-RAY DIFFRACTION87.85
1.65-1.680.31365160.28329861X-RAY DIFFRACTION92.46
1.68-1.70.27885050.26439998X-RAY DIFFRACTION93.24
1.7-1.720.2825480.245610188X-RAY DIFFRACTION96.05
1.72-1.750.26295020.225810304X-RAY DIFFRACTION95.43
1.75-1.770.24715480.214910310X-RAY DIFFRACTION97.37
1.77-1.80.23635660.209410269X-RAY DIFFRACTION95.92
1.8-1.830.23495530.199110308X-RAY DIFFRACTION97.73
1.83-1.860.22185590.199910351X-RAY DIFFRACTION96.32
1.86-1.890.24035420.205310396X-RAY DIFFRACTION97.86
1.89-1.930.23096100.207710294X-RAY DIFFRACTION96.79
1.93-1.970.23995430.209910435X-RAY DIFFRACTION97.74
1.97-2.010.23055490.214410358X-RAY DIFFRACTION97.38
2.01-2.060.24785700.223510405X-RAY DIFFRACTION97.14
2.06-2.110.24125390.212110457X-RAY DIFFRACTION98.26
2.11-2.170.22345700.198410366X-RAY DIFFRACTION97.77
2.17-2.230.22785750.199510472X-RAY DIFFRACTION97.78
2.23-2.30.22885540.198910525X-RAY DIFFRACTION97.91
2.3-2.390.22225370.200410499X-RAY DIFFRACTION98.62
2.39-2.480.24825370.208510534X-RAY DIFFRACTION98.44
2.48-2.590.23575230.203610547X-RAY DIFFRACTION98.55
2.59-2.730.22825260.207410561X-RAY DIFFRACTION98.53
2.73-2.90.23245300.21510604X-RAY DIFFRACTION98.71
2.9-3.130.22255500.213210547X-RAY DIFFRACTION99.03
3.13-3.440.23095320.217510651X-RAY DIFFRACTION99.03
3.44-3.940.21855840.197310629X-RAY DIFFRACTION99.29
3.94-4.960.20755570.187310650X-RAY DIFFRACTION99.29
4.96-48.280.2175540.223610763X-RAY DIFFRACTION99.17

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