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- PDB-9kbb: 3-hydroxyisobutyrate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9kbb
Title3-hydroxyisobutyrate dehydrogenase
Components3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / oxidoreductase activity
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesMicromonospora echinaurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFang, P. / Liu, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Imine Reductase-Catalyzed Remote Stereocontrol for Enantiodivergent Synthesis of Cyclohexylidene-Based Axially Chiral Amines.
Authors: Li, K. / Liu, Z. / Wang, B. / Huang, L. / Yu, L. / Zhou, Z. / Lin, L. / Fang, P. / Fu, H.
History
DepositionOct 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2922
Polymers28,5491
Non-polymers7431
Water4,522251
1
A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules

A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5844
Polymers57,0972
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10570 Å2
ΔGint-94 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.279, 61.652, 60.634
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

21A-643-

HOH

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Components

#1: Protein 3-hydroxyisobutyrate dehydrogenase


Mass: 28548.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinaurantiaca (bacteria)
Gene: GA0070609_2033 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C5HQ65
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Na2HPO4,K2HPO4,BisTris,PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 18, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→47.68 Å / Num. obs: 18833 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 32.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 21.2 / Num. unique obs: 1380 / CC1/2: 0.996 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25.86 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1902 10.1 %
Rwork0.1986 --
obs0.2008 18825 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 48 251 2304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042093
X-RAY DIFFRACTIONf_angle_d0.6852869
X-RAY DIFFRACTIONf_dihedral_angle_d7.762315
X-RAY DIFFRACTIONf_chiral_restr0.038340
X-RAY DIFFRACTIONf_plane_restr0.015374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.26331900.22691667X-RAY DIFFRACTION99.9
2.07-2.150.23911860.21651681X-RAY DIFFRACTION100
2.15-2.250.26031870.20241706X-RAY DIFFRACTION100
2.25-2.370.21691960.20891675X-RAY DIFFRACTION100
2.37-2.520.27751890.2011675X-RAY DIFFRACTION100
2.52-2.710.20221870.20971710X-RAY DIFFRACTION99.9
2.71-2.990.24891840.20521675X-RAY DIFFRACTION99.8
2.99-3.420.21661930.20261712X-RAY DIFFRACTION99.9
3.42-4.30.19081930.17721691X-RAY DIFFRACTION99.8
4.3-25.860.17661970.16851731X-RAY DIFFRACTION99.4

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