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- PDB-9jhz: 3-Hydroxybutyryl-CoA dehydrogenase mutant(S117A) with acetoacetyl... -

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Basic information

Entry
Database: PDB / ID: 9jhz
Title3-Hydroxybutyryl-CoA dehydrogenase mutant(S117A) with acetoacetyl CoA and NAD
Components3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
KeywordsOXIDOREDUCTASE / Complex with acetoacetyl CoA and 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
ACETOACETYL-COENZYME A / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesFaecalibacterium duncaniae
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, J.W. / Jeon, H.J. / 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 10, 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1195
Polymers93,6043
Non-polymers1,5152
Water4,342241
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,23910
Polymers187,2096
Non-polymers3,0304
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,x-y+1,-z1
Buried area20150 Å2
ΔGint-91 kcal/mol
Surface area69500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.562, 90.562, 212.496
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-364-

HOH

31B-555-

HOH

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Components

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


Mass: 31201.486 Da / Num. of mol.: 3 / Mutation: S117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium duncaniae (strain DSM 17677 / JCM 31915 / A2-165) (bacteria)
Gene: FAEPRAA2165_01580 / Production host: Escherichia coli (E. coli) / References: UniProt: C7H5K9
#2: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium citrate dibasic, PEG 3350

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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, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 50628 / % possible obs: 99.5 % / Redundancy: 10.2 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.058 / Rrim(I) all: 0.202 / Χ2: 1.266 / Net I/σ(I): 4.7 / Num. measured all: 515685
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.80.70824320.0250.2220.3810.810.50196.8
2.24-2.284.50.67924430.1360.490.3380.7630.50598
2.28-2.325.20.6425080.1110.4470.2980.7090.48599.3
2.32-2.375.70.625250.2750.6570.2650.6590.47199.4
2.37-2.426.30.60424970.1850.5580.2540.6580.48599.5
2.42-2.486.90.57525010.3570.7260.2290.6210.48999.8
2.48-2.5470.54225380.4150.7660.2130.5850.48599.7
2.54-2.6180.50524980.650.8870.1850.5390.46299.9
2.61-2.699.50.51225560.7170.9140.170.5410.52499.9
2.69-2.7710.10.47724970.770.9330.1530.5020.55999.9
2.77-2.8710.60.42525330.8470.9580.1320.4460.6199.8
2.87-2.9911.10.38125330.9190.9790.1150.3990.65299.8
2.99-3.1210.80.33225400.9410.9850.1020.3480.70599.8
3.12-3.2912.60.26525200.9730.9930.0740.2760.856100
3.29-3.4913.80.22225630.9850.9960.0590.231.09999.9
3.49-3.7614.60.17825530.9890.9970.0460.1841.49100
3.76-4.1414.10.14825590.9930.9980.0390.1531.87999.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.28 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1993 3.95 %
Rwork0.1965 --
obs0.1983 50507 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6526 0 54 241 6821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d10.707919
X-RAY DIFFRACTIONf_chiral_restr0.0471040
X-RAY DIFFRACTIONf_plane_restr0.0041149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.35221260.32443140X-RAY DIFFRACTION91
2.26-2.320.32991460.29733397X-RAY DIFFRACTION98
2.32-2.380.3171430.27223465X-RAY DIFFRACTION99
2.38-2.460.31051460.26483420X-RAY DIFFRACTION100
2.46-2.550.29081390.25273457X-RAY DIFFRACTION100
2.55-2.650.29481410.24663516X-RAY DIFFRACTION100
2.65-2.770.29571380.23253423X-RAY DIFFRACTION100
2.77-2.920.31891450.22723526X-RAY DIFFRACTION100
2.92-3.10.25861410.20943450X-RAY DIFFRACTION100
3.1-3.340.24781440.19963526X-RAY DIFFRACTION100
3.34-3.680.22021430.17753497X-RAY DIFFRACTION100
3.68-4.210.18891470.1543519X-RAY DIFFRACTION100
4.21-5.30.20721470.14213541X-RAY DIFFRACTION100
5.3-45.280.18271470.15673637X-RAY DIFFRACTION100

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