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- PDB-9w61: Butyryl CoA dehydrogenase with FAD -

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Basic information

Entry
Database: PDB / ID: 9w61
TitleButyryl CoA dehydrogenase with FAD
ComponentsButyryl CoA Dehydrogenase with FAD
KeywordsOXIDOREDUCTASE / FAD bound protein
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesFaecalibacterium prausnitzii L2-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butyryl CoA Dehydrogenase with FAD
B: Butyryl CoA Dehydrogenase with FAD
C: Butyryl CoA Dehydrogenase with FAD
D: Butyryl CoA Dehydrogenase with FAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,2188
Polymers170,0764
Non-polymers3,1424
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20470 Å2
ΔGint-138 kcal/mol
Surface area51990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.566, 106.299, 91.954
Angle α, β, γ (deg.)90.00, 117.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Butyryl CoA Dehydrogenase with FAD


Mass: 42518.891 Da / Num. of mol.: 4
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
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: Nov 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 53933 / % possible obs: 87.1 % / Redundancy: 2.8 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.092 / Rrim(I) all: 0.176 / Χ2: 1.877 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.4420.50222310.2720.6540.3620.6240.61371.9
2.44-2.4920.49722030.2110.590.3580.6170.69971.4
2.49-2.531.90.46521990.330.7040.3360.5770.67972
2.53-2.592.10.42923770.530.8320.2960.5250.69377
2.59-2.642.30.42625790.4430.7840.2860.5170.73283.1
2.64-2.72.40.42925750.460.7940.2820.5170.81583.5
2.7-2.772.40.40826020.5490.8420.2720.4940.78884.8
2.77-2.852.50.36426480.6660.8940.2360.4380.82486.1
2.85-2.932.50.3526910.6750.8980.2280.4210.91387.5
2.93-3.022.60.32626990.7140.9130.2090.3911.00987.3
3.02-3.132.70.27827590.8090.9460.1770.3321.17688.8
3.13-3.262.60.24227090.8820.9680.1550.291.40488.2
3.26-3.412.80.19828080.9240.980.1250.2351.6690.3
3.41-3.583.20.18529360.9480.9870.110.2171.78394.9
3.58-3.813.20.15729810.9670.9920.0910.1832.1196.1
3.81-4.13.40.13629370.9720.9930.080.1592.49994.9
4.1-4.523.40.11929700.9790.9950.0690.1382.96395.7
4.52-5.173.30.10529210.9820.9950.0630.1243.0893.7
5.17-6.513.70.10730480.9830.9960.0580.1232.57997.6

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→46.63 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 1953 3.63 %
Rwork0.2192 --
obs0.2209 53814 84.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11607 0 212 275 12094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312019
X-RAY DIFFRACTIONf_angle_d0.63116207
X-RAY DIFFRACTIONf_dihedral_angle_d19.0674615
X-RAY DIFFRACTIONf_chiral_restr0.0411786
X-RAY DIFFRACTIONf_plane_restr0.0042054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.40.3063640.27611694X-RAY DIFFRACTION39
2.4-2.460.30291250.27173139X-RAY DIFFRACTION72
2.46-2.530.28811230.25623233X-RAY DIFFRACTION74
2.53-2.620.27531470.26623581X-RAY DIFFRACTION82
2.62-2.710.31341400.26053711X-RAY DIFFRACTION85
2.71-2.820.32021370.24963751X-RAY DIFFRACTION86
2.82-2.950.28931420.25273874X-RAY DIFFRACTION88
2.95-3.10.29321340.23913863X-RAY DIFFRACTION89
3.1-3.290.29451400.2253915X-RAY DIFFRACTION88
3.29-3.550.27861730.2164146X-RAY DIFFRACTION95
3.55-3.910.24981710.20664197X-RAY DIFFRACTION96
3.91-4.470.22131460.1814213X-RAY DIFFRACTION95
4.47-5.630.23141570.20054203X-RAY DIFFRACTION95

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