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- PDB-9kb0: 3-hydroxyisobutyrate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9kb0
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
Chem-NDP / 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesMicromonospora echinaurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFang, P. / Liu, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of 3-hydroxyisobutyrate dehydrogenase complexing with NADPH
Authors: Fang, P. / Liu, Z.
History
DepositionOct 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyisobutyrate dehydrogenase
C: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2564
Polymers60,7652
Non-polymers1,4912
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-90 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.030, 65.640, 86.670
Angle α, β, γ (deg.)90.00, 100.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-hydroxyisobutyrate dehydrogenase


Mass: 30382.615 Da / Num. of mol.: 2
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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium nitrate, sodium phosphate dibasic, ammonium sulfate, imidazole, MES, PEG 500*MME, PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→65.64 Å / Num. obs: 12620 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.071 / Rrim(I) all: 0.185 / Χ2: 1.01 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2021 / CC1/2: 0.743 / Rpim(I) all: 0.542 / Rrim(I) all: 1.033 / Χ2: 1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→40.26 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 1260 10.01 %
Rwork0.2038 --
obs0.2038 12591 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4138 0 0 37 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094218
X-RAY DIFFRACTIONf_angle_d1.1655780
X-RAY DIFFRACTIONf_dihedral_angle_d15.8861424
X-RAY DIFFRACTIONf_chiral_restr0.053684
X-RAY DIFFRACTIONf_plane_restr0.012754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.020.33091400.30241258X-RAY DIFFRACTION100
3.02-3.150.31981370.28231236X-RAY DIFFRACTION99
3.15-3.320.27921390.2581249X-RAY DIFFRACTION99
3.32-3.530.25861380.23391245X-RAY DIFFRACTION100
3.53-3.80.22971420.22771270X-RAY DIFFRACTION100
3.8-4.180.22351400.21421266X-RAY DIFFRACTION100
4.18-4.790.21931390.18531245X-RAY DIFFRACTION100
4.79-6.020.26371420.2291283X-RAY DIFFRACTION100
6.03-40.260.22051430.191279X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -22.9227 Å / Origin y: -0.9211 Å / Origin z: 18.731 Å
111213212223313233
T0.2963 Å2-0.0121 Å2-0.021 Å2-0.2937 Å20.0068 Å2--0.2983 Å2
L0.3988 °20.0935 °2-0.2261 °2-0.2042 °2-0.1916 °2--0.1699 °2
S-0.0315 Å °0.0556 Å °-0.0016 Å °0.0643 Å °0.0246 Å °0.0213 Å °-0.0307 Å °-0.0466 Å °0 Å °
Refinement TLS groupSelection details: all

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