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- PDB-9w60: Butyryl CoA dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9w60
TitleButyryl CoA dehydrogenase
ComponentsButyryl CoA dehydrogenase apo protein
KeywordsOXIDOREDUCTASE / Apo protein
Biological speciesFaecalibacterium prausnitzii L2-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPark, S.H. / Bang, K.H. / Seo, M.J. / Hwang, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Appl Biol Chem / Year: 2025
Title: Structural insights into butyryl-CoA dehydrogenase and its modeled complex with electron transferring flavoprotein from Faecalibacterium prausnitzii L2-6
Authors: Park, S. / Bang, K. / Shin, B. / Park, I. / Hawkes, H.J.K. / Kim, S. / Hwang, K.Y.
History
DepositionAug 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Butyryl CoA dehydrogenase apo protein
B: Butyryl CoA dehydrogenase apo protein


Theoretical massNumber of molelcules
Total (without water)85,0382
Polymers85,0382
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-18 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.398, 100.398, 163.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

21B-432-

HOH

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Components

#1: Protein Butyryl CoA dehydrogenase apo protein


Mass: 42518.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium prausnitzii L2-6 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: potassium sodium tartrate, 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 PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48 Å / Num. obs: 21233 / % possible obs: 99.6 % / Redundancy: 10.9 % / CC1/2: 0.998 / Net I/σ(I): 8.5
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 1841 / CC1/2: 0.125

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.44 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 1997 9.41 %
Rwork0.2233 --
obs0.2288 21233 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5946 0 0 141 6087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016038
X-RAY DIFFRACTIONf_angle_d1.1058118
X-RAY DIFFRACTIONf_dihedral_angle_d5.066846
X-RAY DIFFRACTIONf_chiral_restr0.057900
X-RAY DIFFRACTIONf_plane_restr0.011048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.34231390.26061347X-RAY DIFFRACTION100
2.87-2.950.36741400.25161340X-RAY DIFFRACTION100
2.95-3.030.29881380.25241341X-RAY DIFFRACTION100
3.03-3.130.33221390.25331343X-RAY DIFFRACTION100
3.13-3.240.31691410.23461360X-RAY DIFFRACTION100
3.24-3.370.31481400.23461347X-RAY DIFFRACTION100
3.37-3.530.26541390.21341343X-RAY DIFFRACTION99
3.53-3.710.28841430.21431370X-RAY DIFFRACTION100
3.71-3.950.31491420.21091375X-RAY DIFFRACTION100
3.95-4.250.24911440.19911368X-RAY DIFFRACTION100
4.25-4.680.24121420.18461375X-RAY DIFFRACTION100
4.68-5.350.25661460.20841397X-RAY DIFFRACTION100
5.35-6.740.25841470.24921419X-RAY DIFFRACTION100
6.74-480.26411570.22981511X-RAY DIFFRACTION99

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