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- PDB-9kbc: 3-hydroxyisobutyrate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9kbc
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
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
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)28,7061
Polymers28,7061
Non-polymers00
Water3,531196
1
A: 3-hydroxyisobutyrate dehydrogenase

A: 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)57,4112
Polymers57,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7990 Å2
ΔGint-85 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.013, 61.597, 60.650
Angle α, β, γ (deg.)90.00, 92.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

21A-483-

HOH

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Components

#1: Protein 3-hydroxyisobutyrate dehydrogenase


Mass: 28705.738 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT pH = 5.0,25% w/v PEG1500

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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 PILATUS 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→47.59 Å / Num. obs: 18747 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Χ2: 0.99 / Net I/σ(I): 16
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 1374 / CC1/2: 0.964 / Rpim(I) all: 0.131 / Rrim(I) all: 0.336 / Χ2: 0.89

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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→25.27 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 1886 10.07 %
Rwork0.2153 --
obs0.218 18728 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→25.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 0 196 2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032046
X-RAY DIFFRACTIONf_angle_d0.5832799
X-RAY DIFFRACTIONf_dihedral_angle_d5.657307
X-RAY DIFFRACTIONf_chiral_restr0.039334
X-RAY DIFFRACTIONf_plane_restr0.011370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.29511780.27031679X-RAY DIFFRACTION99.9
2.07-2.150.29611890.24781666X-RAY DIFFRACTION99.9
2.15-2.250.29131920.24751679X-RAY DIFFRACTION99.8
2.25-2.370.2511870.24171669X-RAY DIFFRACTION99.9
2.37-2.520.25421890.24181686X-RAY DIFFRACTION99.9
2.52-2.710.26241800.23711690X-RAY DIFFRACTION99.9
2.71-2.990.29571870.2331682X-RAY DIFFRACTION99.9
2.99-3.420.24061950.20971700X-RAY DIFFRACTION99.8
3.42-4.30.19831900.18751667X-RAY DIFFRACTION99
4.3-25.270.20291990.17971724X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 12.6112 Å / Origin y: 7.3937 Å / Origin z: 8.7091 Å
111213212223313233
T0.1159 Å20.0102 Å20.0104 Å2-0.0888 Å2-0.0448 Å2--0.0843 Å2
L1.8821 °2-0.7218 °20.862 °2-0.527 °2-0.5217 °2--0.445 °2
S-0.1811 Å °-0.1649 Å °0.0356 Å °0.0587 Å °0.1127 Å °-0.0262 Å °-0.035 Å °-0.0627 Å °-0 Å °
Refinement TLS groupSelection details: all

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