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- PDB-9ji0: 3-Hydroxybutyryl-CoA dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9ji0
Title3-Hydroxybutyryl-CoA dehydrogenase
Components3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
KeywordsOXIDOREDUCTASE / apo protein
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
3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesFaecalibacterium duncaniae
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsYang, J.W. / Jeon, H.J. / Park, S.H. / Jang, S.H. / Park, J.A. / Kim, S.H. / Hwang, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: 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.
History
DepositionSep 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 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


Theoretical massNumber of molelcules
Total (without water)186,8786
Polymers186,8786
Non-polymers00
Water00
1
A: 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

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


Theoretical massNumber of molelcules
Total (without water)186,8786
Polymers186,8786
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area18200 Å2
ΔGint-73 kcal/mol
Surface area67390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.664, 126.609, 108.093
Angle α, β, γ (deg.)90.00, 110.19, 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
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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Lithium sulfate, Tris/HCl, Ammonium sulfate

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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: Apr 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→48.04 Å / Num. obs: 119164 / % possible obs: 98.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 8.14
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 2998 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
PHENIX(1.17rc1_3605: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→48.04 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 33.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 3909 3.28 %
Rwork0.2458 --
obs0.2474 119164 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12930 0 0 0 12930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113116
X-RAY DIFFRACTIONf_angle_d1.11917676
X-RAY DIFFRACTIONf_dihedral_angle_d4.4028040
X-RAY DIFFRACTIONf_chiral_restr0.0572052
X-RAY DIFFRACTIONf_plane_restr0.0072280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.720.37191290.33443357X-RAY DIFFRACTION81
2.72-2.750.32381410.31464124X-RAY DIFFRACTION96
2.75-2.790.35831480.30913982X-RAY DIFFRACTION97
2.79-2.830.34371160.29914154X-RAY DIFFRACTION97
2.83-2.870.34371420.29254092X-RAY DIFFRACTION99
2.87-2.910.36261320.29824261X-RAY DIFFRACTION100
2.91-2.960.32181620.29094106X-RAY DIFFRACTION99
2.96-3.010.33341190.29114210X-RAY DIFFRACTION100
3.01-3.060.34231420.29944174X-RAY DIFFRACTION100
3.06-3.110.36031550.30084117X-RAY DIFFRACTION100
3.11-3.170.37621390.27364203X-RAY DIFFRACTION99
3.17-3.240.35281280.26724199X-RAY DIFFRACTION99
3.24-3.310.27671450.2644102X-RAY DIFFRACTION99
3.31-3.390.3181510.26644227X-RAY DIFFRACTION99
3.39-3.470.321370.25444044X-RAY DIFFRACTION97
3.47-3.560.36621260.24864173X-RAY DIFFRACTION99
3.56-3.670.28961500.23644169X-RAY DIFFRACTION99
3.67-3.790.24691280.22694169X-RAY DIFFRACTION99
3.79-3.920.32961600.23654152X-RAY DIFFRACTION99
3.92-4.080.29731320.24014160X-RAY DIFFRACTION100
4.08-4.260.24441370.21834205X-RAY DIFFRACTION99
4.27-4.490.23561500.21294099X-RAY DIFFRACTION98
4.49-4.770.22351470.20484129X-RAY DIFFRACTION99
4.77-5.140.23751340.21384245X-RAY DIFFRACTION100
5.14-5.660.29431440.23794137X-RAY DIFFRACTION100
5.66-6.470.35551310.26724141X-RAY DIFFRACTION99
6.47-8.150.25741480.2314145X-RAY DIFFRACTION98
8.15-48.040.2671360.20533979X-RAY DIFFRACTION95

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