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- PDB-8zf8: L-methionine oxidase from Burkholderia bacterium, K304A mutant -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8zf8
TitleL-methionine oxidase from Burkholderia bacterium, K304A mutant
ComponentsFAD-binding protein
KeywordsOXIDOREDUCTASE / L-methionine oxidase / FAD-dependent / L-amino acid oxidase
Function / homology
Function and homology information


tryptophan 2-monooxygenase / auxin biosynthetic process / L-amino-acid oxidase activity / amino acid catabolic process
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 2-monooxygenase
Similarity search - Component
Biological speciesBurkholderia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKawamura, Y. / Chisuga, T. / Nakano, S.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K05395 Japan
Japan Society for the Promotion of Science (JSPS)24H01153 Japan
Japan Society for the Promotion of Science (JSPS)23K19283 Japan
Japan Society for the Promotion of Science (JSPS)24K17828 Japan
Japan Science and TechnologyJPMJPR20AB Japan
CitationJournal: J.Biosci.Bioeng. / Year: 2024
Title: Structural and functional analysis of l-methionine oxidase identified through sequence data mining.
Authors: Kawamura, Y. / Sugiura, S. / Araseki, H. / Chisuga, T. / Nakano, S.
History
DepositionMay 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _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: FAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3372
Polymers57,5511
Non-polymers7861
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.031, 122.031, 295.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein FAD-binding protein / L-methionine oxidase


Mass: 57551.293 Da / Num. of mol.: 1 / Mutation: K304A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia (bacteria) / Gene: EKK53_07065 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S0DJC5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 4.78 Å3/Da / Density % sol: 74.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25%(v/v)1,4-Butandiol, 100 mM Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.8 Å / Num. obs: 62033 / % possible obs: 99.9 % / Redundancy: 26.6 % / CC1/2: 0.999 / Net I/σ(I): 26.4
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 123293 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.79 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.278 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23282 3248 5 %RANDOM
Rwork0.20818 ---
obs0.20941 62033 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.409 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å20 Å2-0 Å2
2--2.71 Å2-0 Å2
3----5.42 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 53 52 3950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123999
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163759
X-RAY DIFFRACTIONr_angle_refined_deg1.971.8195442
X-RAY DIFFRACTIONr_angle_other_deg0.651.7498595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9185490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.045537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16410621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
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_it5.0515.6051969
X-RAY DIFFRACTIONr_mcbond_other5.0325.6051969
X-RAY DIFFRACTIONr_mcangle_it6.36710.0482456
X-RAY DIFFRACTIONr_mcangle_other6.36910.0492457
X-RAY DIFFRACTIONr_scbond_it6.1756.0412030
X-RAY DIFFRACTIONr_scbond_other6.1776.0442027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.38210.8612987
X-RAY DIFFRACTIONr_long_range_B_refined9.97752.34427
X-RAY DIFFRACTIONr_long_range_B_other9.98152.34423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 248 -
Rwork0.324 4489 -
obs--99.79 %

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