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- PDB-9gn5: EpxF in complex with FAD from Goodfellowiella coeruleoviolacea -

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Basic information

Entry
Database: PDB / ID: 9gn5
TitleEpxF in complex with FAD from Goodfellowiella coeruleoviolacea
ComponentsEpxF
KeywordsOXIDOREDUCTASE / Natural Product Biosynthesis / Flavoenzyme / Enzyme Mechanism / Structure Function Relationships
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / EpxF
Similarity search - Component
Biological speciesGoodfellowiella coeruleoviolacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWalter, A. / Kuttenlochner, W. / Eisenreich, W. / Groll, M. / Storch, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)325871075 (SFB 1309) Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Studies of alpha ', beta '-Epoxyketone Synthesis by Small-Molecule Flavins and Flavoenzymes.
Authors: Walter, A. / Kuttenlochner, W. / Eisenreich, W. / Yao, C. / Groll, M. / Storch, G.
History
DepositionAug 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EpxF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,68314
Polymers62,0791
Non-polymers2,60413
Water52229
1
A: EpxF
hetero molecules

A: EpxF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,36628
Polymers124,1582
Non-polymers5,20826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area16930 Å2
ΔGint-196 kcal/mol
Surface area39070 Å2
Unit cell
Length a, b, c (Å)131.240, 147.950, 67.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein EpxF


Mass: 62078.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Goodfellowiella coeruleoviolacea (bacteria)
Gene: epxF / Production host: Escherichia coli (E. coli) / References: UniProt: V5RNC8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 100 mM NaCl, 1.8 M (NH4)2SO4, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 25881 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2 / Num. unique obs: 2957 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / SU B: 22.111 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23764 1293 5 %RANDOM
Rwork0.17767 ---
obs0.1806 24574 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---3.76 Å2-0 Å2
3---3.61 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 141 29 4306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0144085
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.6365907
X-RAY DIFFRACTIONr_angle_other_deg1.081.5779339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.315529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.68120.155258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27815685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4591550
X-RAY DIFFRACTIONr_chiral_restr0.040.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024930
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021049
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7115.8932125
X-RAY DIFFRACTIONr_mcbond_other2.7115.8922124
X-RAY DIFFRACTIONr_mcangle_it3.7748.8322651
X-RAY DIFFRACTIONr_mcangle_other3.7748.8332652
X-RAY DIFFRACTIONr_scbond_it2.8426.4252229
X-RAY DIFFRACTIONr_scbond_other2.8426.4262230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9129.5053257
X-RAY DIFFRACTIONr_long_range_B_refined5.21669.4134756
X-RAY DIFFRACTIONr_long_range_B_other5.21669.4214757
X-RAY DIFFRACTIONr_rigid_bond_restr0.5538438
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 94 -
Rwork0.303 1785 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 28.2496 Å / Origin y: 53.8864 Å / Origin z: 6.101 Å
111213212223313233
T0.0108 Å20.0053 Å2-0.0023 Å2-0.0035 Å20.0018 Å2--0.1103 Å2
L0.0949 °2-0.0317 °2-0.0377 °2-0.2716 °2-0.0069 °2--0.1244 °2
S0.0093 Å °-0.0018 Å °0.0111 Å °-0.0183 Å °-0.0035 Å °-0.0035 Å °-0.0289 Å °-0.0114 Å °-0.0057 Å °

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