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

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Basic information

Entry
Database: PDB / ID: 9jhy
Title3-Hydroxybutyryl-CoA dehydrogenase mutant (S117A) with acetoacetyl CoA
Components3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
KeywordsOXIDOREDUCTASE / 3-Hydroxybutyryl-CoA dehydrogenase S117A mutant with acetoacetyl CoA complex
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 / 3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesFaecalibacterium duncaniae
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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)94,0754
Polymers93,2233
Non-polymers8521
Water4,504250
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)188,1498
Polymers186,4466
Non-polymers1,7032
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,x-y+1,-z1
Buried area20850 Å2
ΔGint-61 kcal/mol
Surface area67160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.010, 91.010, 212.700
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-322-

HOH

21A-336-

HOH

31B-565-

HOH

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Components

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


Mass: 31074.303 Da / Num. of mol.: 3
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-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium acetate trihydrate, ammonium sulfate, 20% glycerol, pH 4.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.51 Å / Num. obs: 155255 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 23.1
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3228

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Processing

Software
NameVersionClassification
REFMAC(1.19.1_4122: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.51 Å / Cross valid method: NONE / σ(F): 47.83 / Phase error: 24.1 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2224 1048 0.68 %
Rwork0.1795 --
obs0.2021 155255 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6477 0 0 250 6727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016619
X-RAY DIFFRACTIONf_angle_d1.2648936
X-RAY DIFFRACTIONf_dihedral_angle_d11.546914
X-RAY DIFFRACTIONf_chiral_restr0.071034
X-RAY DIFFRACTIONf_plane_restr0.0091139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-20.29711460.30721948X-RAY DIFFRACTION99
2-2.130.33241540.287822059X-RAY DIFFRACTION99
2.13-2.290.29811440.262722037X-RAY DIFFRACTION99
2.29-2.520.28341520.244922023X-RAY DIFFRACTION99
2.52-2.880.24551480.214222033X-RAY DIFFRACTION99
2.88-3.630.2511540.173522072X-RAY DIFFRACTION99
3.63-45.510.21211500.150322035X-RAY DIFFRACTION99

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