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- PDB-7pbg: 4-ethylphenol oxidase from Gulosibacter chungangensis: native str... -

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Basic information

Entry
Database: PDB / ID: 7pbg
Title4-ethylphenol oxidase from Gulosibacter chungangensis: native structure
ComponentsFAD-binding oxidoreductase
KeywordsOXIDOREDUCTASE / flavoprotein / biocatalysis / genome mining / enzyme structure / 4-vinylphenol / dehydrogenation / 4-alkylphenol oxidase
Function / homology
Function and homology information


catalytic activity / FAD binding
Similarity search - Function
Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-binding oxidoreductase
Similarity search - Component
Biological speciesGulosibacter chungangensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAlvigini, L. / Mattevi, A.
Funding support1items
OrganizationGrant numberCountry
European Union (EU)Bio Based Industries Joint Undertaking under the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 837890 (SMARTBOX)
CitationJournal: Chembiochem / Year: 2021
Title: Discovery, Biocatalytic Exploration and Structural Analysis of a 4-Ethylphenol Oxidase from Gulosibacter chungangensis.
Authors: Alvigini, L. / Gran-Scheuch, A. / Guo, Y. / Trajkovic, M. / Saifuddin, M. / Fraaije, M.W. / Mattevi, A.
History
DepositionAug 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-binding oxidoreductase
B: FAD-binding oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7516
Polymers118,1092
Non-polymers1,6424
Water16,646924
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-96 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.134, 96.080, 87.636
Angle α, β, γ (deg.)90.000, 115.650, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FAD-binding oxidoreductase


Mass: 59054.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gulosibacter chungangensis (bacteria) / Gene: F8O05_00770 / Production host: Escherichia coli (E. coli) / Variant (production host): NEB 10beta cells / References: UniProt: A0A7J5BGR1
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Trizma pH 8.0, 24% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999869 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999869 Å / Relative weight: 1
ReflectionResolution: 1.6→44.23 Å / Num. obs: 140211 / % possible obs: 94.5 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Rrim(I) all: 0.092 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.642 / Num. unique obs: 6353 / CC1/2: 0.71 / Rpim(I) all: 0.353 / Rrim(I) all: 0.738 / % possible all: 86.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FXD

5fxd


Resolution: 1.6→44.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.939 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 6975 5 %RANDOM
Rwork0.1809 ---
obs0.1822 133003 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.58 Å2 / Biso mean: 21.958 Å2 / Biso min: 15.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.54 Å2
2---1.62 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 1.6→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8200 0 108 924 9232
Biso mean--19.39 33.12 -
Num. residues----1050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177598
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.64711604
X-RAY DIFFRACTIONr_angle_other_deg1.5351.57117624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68151048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3621.966468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.928151334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0261562
X-RAY DIFFRACTIONr_chiral_restr0.0870.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021830
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 483 -
Rwork0.249 9018 -
all-9501 -
obs--87 %

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