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- PDB-9w58: Structure of L-glutamate oxidase E617K mutant -

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Basic information

Entry
Database: PDB / ID: 9w58
TitleStructure of L-glutamate oxidase E617K mutant
Components(L-glutamate oxidase precursor) 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 / L-glutamate oxidase precursor
Similarity search - Component
Biological speciesStreptomyces sp. X-119-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,4708
Polymers143,8996
Non-polymers1,5712
Water26,4281467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45130 Å2
ΔGint-210 kcal/mol
Surface area41370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.800, 128.900, 150.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein L-glutamate oxidase precursor / LGOX


Mass: 42019.227 Da / Num. of mol.: 2
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: plasmid / Details (production host): 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.: 2
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: plasmid / Details (production host): 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: 19354.248 Da / Num. of mol.: 2 / Mutation: E617K
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) with E617K mutation.
Source: (gene. exp.) Streptomyces sp. X-119-6 (bacteria) / Strain: X-119-6 / Gene: lgoX / Plasmid: plasmid / Details (production host): pMal-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8L3C7, L-glutamate oxidase
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1467 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1 M CAPS (pH 10.5), 20% (w/v) PEG8000, and 0.02 M NaCl

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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: Jun 22, 2023
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→75.39 Å / Num. obs: 115098 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 13.69 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4 / Num. unique obs: 5646 / CC1/2: 0.916 / % possible all: 100

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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: 1.85→65.08 Å / SU ML: 0.1531 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.1494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1871 5747 5 %
Rwork0.1526 109236 -
obs0.1543 114983 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.89 Å2
Refinement stepCycle: LAST / Resolution: 1.85→65.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9612 0 106 1467 11185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007410202
X-RAY DIFFRACTIONf_angle_d0.85513912
X-RAY DIFFRACTIONf_chiral_restr0.05561459
X-RAY DIFFRACTIONf_plane_restr0.00891825
X-RAY DIFFRACTIONf_dihedral_angle_d13.40913776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.21291910.18643648X-RAY DIFFRACTION100
1.87-1.890.24732050.18873564X-RAY DIFFRACTION99.97
1.89-1.920.21241910.18563593X-RAY DIFFRACTION100
1.92-1.940.2182000.18053561X-RAY DIFFRACTION100
1.94-1.970.22681950.17443645X-RAY DIFFRACTION100
1.97-1.990.22291810.16313564X-RAY DIFFRACTION99.97
1.99-2.020.20652200.15813619X-RAY DIFFRACTION100
2.02-2.050.20231880.16023588X-RAY DIFFRACTION99.97
2.05-2.080.20811810.15583622X-RAY DIFFRACTION99.95
2.08-2.120.19641920.15043603X-RAY DIFFRACTION99.97
2.12-2.150.16791810.15023618X-RAY DIFFRACTION100
2.15-2.190.18331890.14973588X-RAY DIFFRACTION100
2.19-2.240.19511850.15483634X-RAY DIFFRACTION99.97
2.24-2.280.20311720.15923643X-RAY DIFFRACTION99.95
2.28-2.330.19272010.15223573X-RAY DIFFRACTION100
2.33-2.390.21231850.15493652X-RAY DIFFRACTION100
2.39-2.440.18011870.15723621X-RAY DIFFRACTION100
2.44-2.510.21052130.1523605X-RAY DIFFRACTION99.97
2.51-2.580.18941940.15953603X-RAY DIFFRACTION100
2.58-2.670.17821920.15743646X-RAY DIFFRACTION100
2.67-2.760.19261780.14963673X-RAY DIFFRACTION100
2.76-2.870.19512050.15443630X-RAY DIFFRACTION99.97
2.87-30.2032000.15293640X-RAY DIFFRACTION100
3-3.160.18551650.15323658X-RAY DIFFRACTION100
3.16-3.360.15941860.14773675X-RAY DIFFRACTION100
3.36-3.620.16931940.14323687X-RAY DIFFRACTION100
3.62-3.990.1682030.13373670X-RAY DIFFRACTION100
3.99-4.560.15051790.12053740X-RAY DIFFRACTION100
4.56-5.750.1591860.1393763X-RAY DIFFRACTION100
5.75-65.080.18792080.17613910X-RAY DIFFRACTION99.76

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