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- PDB-8zb2: L-Methionine oxidase from Burkholderiales bacterium -

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Basic information

Entry
Database: PDB / ID: 8zb2
TitleL-Methionine oxidase from Burkholderiales bacterium
ComponentsFAD-binding protein
KeywordsOXIDOREDUCTASE / L-Methionine / FAD-dependent / 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 / THIOCYANATE ION / Tryptophan 2-monooxygenase
Similarity search - Component
Biological speciesBurkholderiales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKawamura, Y. / Chisuga, T. / Nakano, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K05395 Japan
Japan Society for the Promotion of Science (JSPS)24H01153 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
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 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: FAD-binding protein
B: FAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9556
Polymers112,2682
Non-polymers1,6874
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-11 kcal/mol
Surface area38880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.788, 124.788, 148.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 2 - 507 / Label seq-ID: 1 - 506

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein FAD-binding protein


Mass: 56133.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderiales bacterium (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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% (v/v) PEG 3350, 0.2 M Potassium nitrate, and 0.2 M potassium thiocyanate

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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 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→47.784 Å / Num. obs: 36298 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 75.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.5
Reflection shellResolution: 2.69→2.84 Å / Rmerge(I) obs: 1.313 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5286 / CC1/2: 0.807

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→47.78 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 20.332 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R: 0.906 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28316 1770 4.9 %RANDOM
Rwork0.22039 ---
obs0.22343 34446 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.69→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 112 0 7751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137948
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177467
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.63710802
X-RAY DIFFRACTIONr_angle_other_deg1.2011.57517075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4665968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92720.317442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.05151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0771576
X-RAY DIFFRACTIONr_chiral_restr0.1250.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021964
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_it8.6039.1473895
X-RAY DIFFRACTIONr_mcbond_other8.5949.1483892
X-RAY DIFFRACTIONr_mcangle_it12.35113.7134854
X-RAY DIFFRACTIONr_mcangle_other12.3513.7134855
X-RAY DIFFRACTIONr_scbond_it7.7049.4974053
X-RAY DIFFRACTIONr_scbond_other7.6959.4984048
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.45914.0435947
X-RAY DIFFRACTIONr_long_range_B_refined15.3518842
X-RAY DIFFRACTIONr_long_range_B_other15.358843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15059 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.692→2.762 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 119 -
Rwork0.38 2556 -
obs--99.41 %

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