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- PDB-9w54: Structure of L-glutamate oxidase in complex with L-glutamate -

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Basic information

Entry
Database: PDB / ID: 9w54
TitleStructure of L-glutamate oxidase in complex with L-glutamate
Components(L-glutamate oxidase ...) x 3
KeywordsOXIDOREDUCTASE / L-glutamic acid oxidase
Function / homology
Function and homology information


L-glutamate oxidase / L-amino-acid oxidase activity / amino acid catabolic process / nucleotide binding / extracellular region
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / GLUTAMIC ACID / L-glutamate oxidase precursor
Similarity search - Component
Biological speciesStreptomyces sp. X-119-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsUeda, Y. / Takekawa, N. / Nakayama, N. / Inagaki, K. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K05278 Japan
CitationJournal: Protein Sci. / Year: 2026
Title: Substrate recognition mechanisms of ʟ-glutamate oxidase from Streptomyces sp. and its conversion to ʟ-tyrosine oxidase.
Authors: Ueda, Y. / Yano, Y. / Nakayama, N. / Takekawa, N. / Inagaki, K. / Imada, K.
History
DepositionAug 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-glutamate oxidase precursor
B: L-glutamate oxidase precursor
C: L-glutamate oxidase precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9805
Polymers70,0473
Non-polymers9332
Water3,945219
1
A: L-glutamate oxidase precursor
B: L-glutamate oxidase precursor
C: L-glutamate oxidase precursor
hetero molecules

A: L-glutamate oxidase precursor
B: L-glutamate oxidase precursor
C: L-glutamate oxidase precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,95910
Polymers140,0946
Non-polymers1,8654
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area45710 Å2
ΔGint-209 kcal/mol
Surface area40810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.310, 124.310, 168.801
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Components on special symmetry positions
IDModelComponents
11A-971-

HOH

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Components

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L-glutamate oxidase ... , 3 types, 3 molecules ABC

#1: Protein L-glutamate oxidase precursor / LGOX


Mass: 42019.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The L-glutamate oxidase alpha fragment (A15-Y390) produced by proteolytic processing of the L-glutamate oxidase precursor (uniprot ID:Q8L3C7).
Source: (gene. exp.) Streptomyces sp. X-119-6 (bacteria) / Strain: X-119-6 / Gene: lgoX / Plasmid: pMal-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8L3C7, L-glutamate oxidase
#2: Protein L-glutamate oxidase precursor / LGOX


Mass: 10575.776 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The L-glutamate oxidase gamma fragment (A391-A480) produced by proteolytic processing of the L-glutamate oxidase precursor (uniprot ID:Q8L3C7).
Source: (gene. exp.) Streptomyces sp. X-119-6 (bacteria) / Strain: X-119-6 / Gene: lgoX / Plasmid: pMal-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8L3C7, L-glutamate oxidase
#3: Protein L-glutamate oxidase precursor / LGOX


Mass: 17452.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The L-glutamate oxidase beta fragment (G521-G683) produced by proteolytic processing of the L-glutamate oxidase precursor (uniprot ID:Q8L3C7).
Source: (gene. exp.) Streptomyces sp. X-119-6 (bacteria) / Strain: X-119-6 / Gene: lgoX / Plasmid: pMal-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8L3C7, L-glutamate oxidase

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Non-polymers , 3 types, 221 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M CAPS pH10, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2022
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→62.16 Å / Num. obs: 25482 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.967 / Net I/σ(I): 8.2
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3022 / CC1/2: 0.72 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1M

2e1m


Resolution: 2.55→62.15 Å / SU ML: 0.3324 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 1999 7.86 %
Rwork0.1921 23432 -
obs0.1962 25431 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.41 Å2
Refinement stepCycle: LAST / Resolution: 2.55→62.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 63 219 5089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00265006
X-RAY DIFFRACTIONf_angle_d0.59586824
X-RAY DIFFRACTIONf_chiral_restr0.0417715
X-RAY DIFFRACTIONf_plane_restr0.0047895
X-RAY DIFFRACTIONf_dihedral_angle_d13.84861848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.36821380.28591619X-RAY DIFFRACTION98.43
2.61-2.680.32081410.27271642X-RAY DIFFRACTION98.78
2.68-2.760.31671420.24111670X-RAY DIFFRACTION99.72
2.76-2.850.28651400.23071643X-RAY DIFFRACTION99.89
2.85-2.950.27051430.22911672X-RAY DIFFRACTION99.89
2.95-3.070.29681410.23631651X-RAY DIFFRACTION99.89
3.07-3.210.32631420.23061672X-RAY DIFFRACTION99.67
3.21-3.380.28641440.2161681X-RAY DIFFRACTION99.89
3.38-3.590.25181430.19011683X-RAY DIFFRACTION99.95
3.59-3.870.2351440.17531690X-RAY DIFFRACTION100
3.87-4.260.191450.14931693X-RAY DIFFRACTION99.73
4.26-4.880.18321460.14011710X-RAY DIFFRACTION98.93
4.88-6.140.20211420.1631663X-RAY DIFFRACTION95.4
6.14-62.150.22971480.18571743X-RAY DIFFRACTION92.79

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