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- PDB-9w15: 3-Hydroxybutyryl-CoA dehydrogenase with NAD and acetoacetyl CoA -

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Basic information

Entry
Database: PDB / ID: 9w15
Title3-Hydroxybutyryl-CoA dehydrogenase with NAD and acetoacetyl CoA
Components3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
KeywordsOXIDOREDUCTASE / NAD and acetoacetyl-CoA complex
Function / homologyACETOACETYL-COENZYME A / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesFaecalibacterium prausnitzii L2-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 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

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Assembly

Deposited unit
B: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,71614
Polymers186,6566
Non-polymers6,0608
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27820 Å2
ΔGint-79 kcal/mol
Surface area63690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.623, 92.142, 132.473
Angle α, β, γ (deg.)90.00, 100.42, 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


Mass: 31109.393 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium prausnitzii L2-6 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H40N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% (v/v) PEG 550 MME, 0.05 M magnesium chloride, and 0.1 M HEPES-NaOH (pH 7.5)

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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 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.29→50 Å / Num. obs: 27041 / % possible obs: 90 % / Redundancy: 3.4 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.077 / Rrim(I) all: 0.162 / Χ2: 1.01 / Net I/σ(I): 4.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.29-3.3620.39511250.1990.5770.3040.5020.42875.4
3.36-3.4220.35211130.2610.6440.2670.4450.31874.8
3.42-3.482.10.32310680.260.6430.2370.4040.31971.2
3.48-3.552.30.3312820.3090.6870.2330.4070.34285.6
3.55-3.632.50.3412920.3810.7430.2350.4170.40288
3.63-3.722.60.32413610.4540.790.2160.3920.45491.5
3.72-3.812.80.30213400.5680.8510.1960.3630.45388.9
3.81-3.912.90.2913310.6490.8870.180.3440.52490.4
3.91-4.0330.27414070.7240.9160.1680.3240.52291.9
4.03-4.163.20.25813790.780.9360.1530.3020.5992.8
4.16-4.313.50.22713840.8810.9680.1270.2620.75293.5
4.31-4.483.50.21713810.8940.9720.1210.250.86891.7
4.48-4.683.60.19313550.9250.980.1060.2220.86791.1
4.68-4.934.10.18614620.9420.9850.0980.2110.96596.4
4.93-5.243.90.18814410.9530.9880.0990.2140.92196.3
5.24-5.643.90.18414440.9450.9860.0970.2090.87296.3
5.64-6.2140.17614560.9450.9860.0930.20.85595.7
6.21-7.140.13314040.9730.9930.0690.1511.05892.9
7.1-8.945.40.09214990.9910.9980.0420.1011.72898.2
8.94-505.50.07415170.9930.9980.0330.0812.45196.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→48.01 Å / SU ML: 0.62 / Cross valid method: NONE / σ(F): 1.44 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 2000 7.4 %
Rwork0.2526 --
obs0.2557 27024 89.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.29→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12918 0 392 0 13310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213508
X-RAY DIFFRACTIONf_angle_d0.53418228
X-RAY DIFFRACTIONf_dihedral_angle_d8.3392004
X-RAY DIFFRACTIONf_chiral_restr0.0432086
X-RAY DIFFRACTIONf_plane_restr0.0052294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.380.41141100.37371380X-RAY DIFFRACTION70
3.47-3.570.35171340.31691657X-RAY DIFFRACTION84
3.57-3.690.38641420.30921787X-RAY DIFFRACTION90
3.69-3.820.35291400.29321761X-RAY DIFFRACTION89
3.82-3.970.33841450.25631812X-RAY DIFFRACTION91
3.97-4.150.30461480.25621848X-RAY DIFFRACTION92
4.15-4.370.28051490.24311862X-RAY DIFFRACTION93
4.37-4.640.28751430.23621785X-RAY DIFFRACTION90
4.64-50.26211530.21251915X-RAY DIFFRACTION97
5-5.50.28111540.2421930X-RAY DIFFRACTION96
5.5-6.30.32831540.23911919X-RAY DIFFRACTION96

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