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- PDB-9jhe: 3-hydroxybutyryl-CoA dehydrogenase with NAD -

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Basic information

Entry
Database: PDB / ID: 9jhe
Title3-hydroxybutyryl-CoA dehydrogenase with NAD
Components3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
KeywordsOXIDOREDUCTASE / Complex with NAD
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydrogenase activity / fatty acid beta-oxidation / NAD+ binding
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesFaecalibacterium duncaniae
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPark, J.A. / Yang, J.W. / Park, S.H. / Kim, S.H. / Hwang, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Citation
Journal: Int J Mol Sci / Year: 2024
Title: Structural Insights and Catalytic Mechanism of 3-Hydroxybutyryl-CoA Dehydrogenase from Faecalibacterium Prausnitzii A2-165.
Authors: Yang, J. / Jeon, H.J. / Park, S. / Park, J. / Jang, S. / Shin, B. / Bang, K. / Hawkes, H.K. / Park, S. / Kim, S. / Hwang, K.Y.
#1: Journal: Int J Mol Sci / Year: 2024
Title: Structural Insights and Catalytic Mechanism of 3-Hydroxybutyryl-CoA Dehydrogenase from
Authors: Yang, J. / Jeon, H.J. / Park, S. / Park, J. / Jang, S. / Shin, B. / Bang, K. / Hawkes, H.K. / Park, S. / Kim, S. / Hwang, K.Y.
History
DepositionSep 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 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-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
D: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
E: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
F: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,85912
Polymers186,8786
Non-polymers3,9816
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24830 Å2
ΔGint-128 kcal/mol
Surface area66590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.821, 80.476, 128.345
Angle α, β, γ (deg.)90.00, 102.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31146.408 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium duncaniae (strain DSM 17677 / JCM 31915 / A2-165) (bacteria)
Gene: FAEPRAA2165_01580, GXM22_07070 / Production host: Escherichia coli (E. coli)
References: UniProt: C7H5K9, 3-hydroxybutyryl-CoA dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, bis-tris/HCl, PEG 3,350

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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 PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→46.7 Å / Num. obs: 54528 / % possible obs: 91.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.9
Reflection shellResolution: 2.55→2.55 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 12.8 / Num. unique obs: 2381

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→46.64 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.51 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 2000 3.67 %
Rwork0.2125 --
obs0.2144 54528 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12978 0 264 78 13320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d7.2411836
X-RAY DIFFRACTIONf_chiral_restr0.0452106
X-RAY DIFFRACTIONf_plane_restr0.0052298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.37641230.31643253X-RAY DIFFRACTION79
2.61-2.680.36551280.30813342X-RAY DIFFRACTION83
2.68-2.760.35371300.28913419X-RAY DIFFRACTION84
2.76-2.850.33741360.2743580X-RAY DIFFRACTION88
2.85-2.950.32471370.26873568X-RAY DIFFRACTION88
2.95-3.070.30561420.26663725X-RAY DIFFRACTION91
3.07-3.210.3181440.26853789X-RAY DIFFRACTION93
3.21-3.380.31081450.24993820X-RAY DIFFRACTION94
3.38-3.590.3211490.2353920X-RAY DIFFRACTION97
3.59-3.870.30961520.21953983X-RAY DIFFRACTION98
3.87-4.260.23461520.19293998X-RAY DIFFRACTION98
4.26-4.870.23091530.17324004X-RAY DIFFRACTION97
4.87-6.140.25071530.18694015X-RAY DIFFRACTION97

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