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- PDB-9w17: 3-Hydroxybutyryl-CoA dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9w17
Title3-Hydroxybutyryl-CoA dehydrogenase
Components3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
KeywordsOXIDOREDUCTASE / Apo structure
Biological speciesFaecalibacterium prausnitzii L2-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsShin, B.M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Structural Basis for Substrate-Induced Activation of 3-Hydroxybutyryl-CoA Dehydrogenase from Faecalibacterium prausnitzii L2-6
Authors: Shin, B.M. / Park, S.H. / Park, I.G. / Bang, K.H. / Kim, S.H. / Hwang, K.Y.
History
DepositionJul 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
A: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
B: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein


Theoretical massNumber of molelcules
Total (without water)93,3283
Polymers93,3283
Non-polymers00
Water4,179232
1
C: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
A: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
B: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein

C: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
A: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
B: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein


Theoretical massNumber of molelcules
Total (without water)186,6566
Polymers186,6566
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area18300 Å2
ΔGint-74 kcal/mol
Surface area68220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.505, 143.747, 168.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-349-

HOH

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Components

#1: Protein 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein


Mass: 31109.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium prausnitzii L2-6 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) PEG 3350, 0.2 M magnesium chloride, and 0.1 M Tris-HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 42280 / % possible obs: 94.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.4
Reflection shellResolution: 2.29→2.34 Å / Rmerge(I) obs: 0.43 / Num. unique obs: 1827

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→46.3 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 2000 4.73 %
Rwork0.2177 --
obs0.22 42250 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6483 0 0 232 6715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046570
X-RAY DIFFRACTIONf_angle_d0.6358835
X-RAY DIFFRACTIONf_dihedral_angle_d6.775903
X-RAY DIFFRACTIONf_chiral_restr0.0421023
X-RAY DIFFRACTIONf_plane_restr0.011134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.36061200.33262409X-RAY DIFFRACTION80
2.35-2.410.33851310.30432658X-RAY DIFFRACTION88
2.41-2.480.32351330.27692660X-RAY DIFFRACTION89
2.48-2.560.31331350.26272731X-RAY DIFFRACTION90
2.56-2.660.32721420.26232847X-RAY DIFFRACTION95
2.66-2.760.34541430.26352885X-RAY DIFFRACTION95
2.76-2.890.28741440.24782898X-RAY DIFFRACTION96
2.89-3.040.30881450.23762911X-RAY DIFFRACTION96
3.04-3.230.2881450.23192925X-RAY DIFFRACTION96
3.23-3.480.30681480.22082984X-RAY DIFFRACTION98
3.48-3.830.24361510.19043023X-RAY DIFFRACTION99
3.83-4.380.23421500.17573031X-RAY DIFFRACTION99
4.38-5.520.22231530.17543077X-RAY DIFFRACTION99

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