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- PDB-8z0x: Crystal structure of glyoxylate reductase from Acetobacter aceti ... -

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Basic information

Entry
Database: PDB / ID: 8z0x
TitleCrystal structure of glyoxylate reductase from Acetobacter aceti in the apo form
Components3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / glyoxylate reductase apo 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
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: To Be Published
Title: Crystal structure of glyoxylate reductase from Acetobacter aceti
Authors: Majumder, T.R. / Yoshizawa, T. / Inoue, M. / Aono, R. / Matsumura, H. / Mihara, H.
History
DepositionApr 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)263,9198
Polymers263,9198
Non-polymers00
Water21,5461196
1
A: 3-hydroxyisobutyrate dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase
C: 3-hydroxyisobutyrate dehydrogenase
D: 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)131,9594
Polymers131,9594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-105 kcal/mol
Surface area38290 Å2
MethodPISA
2
E: 3-hydroxyisobutyrate dehydrogenase
F: 3-hydroxyisobutyrate dehydrogenase
G: 3-hydroxyisobutyrate dehydrogenase
H: 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)131,9594
Polymers131,9594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-106 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.454, 191.880, 117.846
Angle α, β, γ (deg.)90.000, 94.990, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1196 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.18 %
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→48.18 Å / Num. obs: 330996 / % possible obs: 99.38 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.64 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1753 / Rpim(I) all: 0.07217 / Rrim(I) all: 0.1898 / Net I/σ(I): 25.63
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.6553 / Mean I/σ(I) obs: 7.17 / Num. unique obs: 32100 / CC1/2: 0.769 / CC star: 0.932 / Rpim(I) all: 0.3395 / Rrim(I) all: 0.7428 / % possible all: 96.54

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.18 Å / SU ML: 0.1524 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2207 16539 5 %
Rwork0.2015 314315 -
obs0.2025 330854 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15620 0 0 1196 16816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006515867
X-RAY DIFFRACTIONf_angle_d0.964821548
X-RAY DIFFRACTIONf_chiral_restr0.05392590
X-RAY DIFFRACTIONf_plane_restr0.00892800
X-RAY DIFFRACTIONf_dihedral_angle_d5.31482271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.23475070.2029690X-RAY DIFFRACTION92.73
1.62-1.640.22885400.198110318X-RAY DIFFRACTION97.11
1.64-1.660.22875490.193910416X-RAY DIFFRACTION99.76
1.66-1.680.21985520.18310496X-RAY DIFFRACTION99.95
1.68-1.70.22475560.185610557X-RAY DIFFRACTION99.97
1.7-1.720.21685510.1810472X-RAY DIFFRACTION99.95
1.72-1.750.21535570.179910583X-RAY DIFFRACTION99.97
1.75-1.770.20915520.184410483X-RAY DIFFRACTION99.98
1.77-1.80.20475560.19210568X-RAY DIFFRACTION99.97
1.8-1.830.22085530.194810511X-RAY DIFFRACTION99.96
1.83-1.860.23145540.204710537X-RAY DIFFRACTION99.95
1.86-1.90.22745530.211110505X-RAY DIFFRACTION99.94
1.9-1.930.23175530.206210511X-RAY DIFFRACTION99.88
1.93-1.970.23185560.207210553X-RAY DIFFRACTION99.87
1.97-2.020.23825520.203610480X-RAY DIFFRACTION99.8
2.02-2.060.22165550.199210548X-RAY DIFFRACTION99.82
2.06-2.110.23585510.200810487X-RAY DIFFRACTION99.72
2.11-2.170.21825510.198310461X-RAY DIFFRACTION99.62
2.17-2.240.21615530.193910517X-RAY DIFFRACTION99.56
2.24-2.310.23185540.197210511X-RAY DIFFRACTION99.53
2.31-2.390.23075530.200210525X-RAY DIFFRACTION99.6
2.39-2.490.20175510.201610458X-RAY DIFFRACTION99.56
2.49-2.60.21115530.201210507X-RAY DIFFRACTION99.55
2.6-2.740.22185540.198510520X-RAY DIFFRACTION99.49
2.74-2.910.25015510.210310469X-RAY DIFFRACTION99.5
2.91-3.130.20935520.207810484X-RAY DIFFRACTION99.37
3.13-3.450.22165520.210810498X-RAY DIFFRACTION99.25
3.45-3.950.22285540.19910515X-RAY DIFFRACTION99.57
3.95-4.970.19865550.192510554X-RAY DIFFRACTION99.51
4.97-48.180.22125590.224810581X-RAY DIFFRACTION99.03

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