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- PDB-7e0c: Structure of L-glutamate oxidase R305E mutant -

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Basic information

Entry
Database: PDB / ID: 7e0c
TitleStructure of L-glutamate oxidase R305E mutant
ComponentsL-glutamate oxidase
KeywordsOXIDOREDUCTASE / L-glutamic acid oxidase / L-amino 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: 2.65 Å
AuthorsIto, N. / Matsuo, S. / Inagaki, K. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24560962 Japan
CitationJournal: Protein Sci. / Year: 2021
Title: A new l-arginine oxidase engineered from l-glutamate oxidase.
Authors: Yano, Y. / Matsuo, S. / Ito, N. / Tamura, T. / Kusakabe, H. / Inagaki, K. / Imada, K.
History
DepositionJan 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-glutamate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2132
Polymers76,4271
Non-polymers7861
Water1,56787
1
A: L-glutamate oxidase
hetero molecules

A: L-glutamate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,4264
Polymers152,8552
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area8310 Å2
ΔGint-19 kcal/mol
Surface area43960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.970, 123.970, 168.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1069-

HOH

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Components

#1: Protein L-glutamate oxidase


Mass: 76427.250 Da / Num. of mol.: 1 / Mutation: R305E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. X-119-6 (bacteria) / Gene: Lgox / Plasmid: pMal-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8L3C7, L-glutamate oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12% (w/v) PEG 8000, 0.1M Tris-HCl pH7.0, 75mM MgCl2

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2016
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→84.3 Å / Num. obs: 22897 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 36.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.034 / Net I/σ(I): 18.5
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 13 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2970 / CC1/2: 0.93 / Rpim(I) all: 0.191 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
BSSdata collection
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1M

2e1m


Resolution: 2.65→66.311 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1148 5.02 %
Rwork0.1908 --
obs0.1934 22853 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→66.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 53 87 4822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064917
X-RAY DIFFRACTIONf_angle_d0.866711
X-RAY DIFFRACTIONf_dihedral_angle_d6.9983959
X-RAY DIFFRACTIONf_chiral_restr0.051704
X-RAY DIFFRACTIONf_plane_restr0.006879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.77060.29661360.21632638X-RAY DIFFRACTION100
2.7706-2.91670.28771530.21542645X-RAY DIFFRACTION100
2.9167-3.09940.31991300.21242691X-RAY DIFFRACTION100
3.0994-3.33870.26271420.19842657X-RAY DIFFRACTION100
3.3387-3.67470.20451270.17512705X-RAY DIFFRACTION100
3.6747-4.20630.19221440.16592718X-RAY DIFFRACTION100
4.2063-5.29920.20681430.16492741X-RAY DIFFRACTION100
5.2992-66.3110.2631730.22182910X-RAY DIFFRACTION100

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