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- PDB-8jpw: Crystal Structure of Single-chain L-Glutamate Oxidase Mutant from... -

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Basic information

Entry
Database: PDB / ID: 8jpw
TitleCrystal Structure of Single-chain L-Glutamate Oxidase Mutant from Streptomyces sp. X-119-6
ComponentsL-glutamate oxidase
KeywordsOXIDOREDUCTASE / amino acid oxidase / mutant
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
2-OXOGLUTARIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / L-glutamate oxidase precursor
Similarity search - Component
Biological speciesStreptomyces sp. X-119-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsYamaguchi, H. / Takahashi, K. / Tatsumi, M. / Tagami, U. / Mizukoshi, T. / Miyano, H. / Sugiki, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Enzyme.Microb.Technol. / Year: 2023
Title: Development of a novel single-chain l-glutamate oxidase from Streptomyces sp. X-119-6 by inserting flexible linkers.
Authors: Yamaguchi, H. / Takahashi, K. / Tatsumi, M. / Tagami, U. / Mizukoshi, T. / Miyano, H. / Sugiki, M.
History
DepositionJun 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Refinement description / Category: chem_comp_atom / chem_comp_bond / refine
Item: _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)74,3695
Polymers73,3071
Non-polymers1,0624
Water3,315184
1
A: L-glutamate oxidase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)594,95340
Polymers586,4538
Non-polymers8,50032
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area45880 Å2
ΔGint-573 kcal/mol
Surface area171790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.400, 158.400, 138.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-804-

HOH

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Components

#1: Protein L-glutamate oxidase


Mass: 73306.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. X-119-6 (bacteria) / Gene: Lgox / Production host: Escherichia coli (E. coli) / References: UniProt: Q8L3C7
#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: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate trihydrate (pH 4.5), 10% PEG3000 and 0.05 M zinc acetate dihydrate

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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 S 6M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→49.32 Å / Num. obs: 25525 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 20
Reflection shellResolution: 2.66→2.79 Å / Num. unique obs: 3346 / CC1/2: 0.818

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→49.32 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.878 / SU B: 8.584 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.305 1188 -
Rwork0.259 --
obs-24275 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-15 Å20 Å20 Å2
2--15 Å20 Å2
3----29.99 Å2
Refinement stepCycle: 1 / Resolution: 2.66→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 65 184 4940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
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_it5.0035.4232375
X-RAY DIFFRACTIONr_mcbond_other55.4232375
X-RAY DIFFRACTIONr_mcangle_it7.1979.7272960
X-RAY DIFFRACTIONr_mcangle_other7.1969.7272961
X-RAY DIFFRACTIONr_scbond_it5.2985.8012520
X-RAY DIFFRACTIONr_scbond_other5.2925.82518
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0110.4563710
X-RAY DIFFRACTIONr_long_range_B_refined11.12154.225804
X-RAY DIFFRACTIONr_long_range_B_other11.09454.155786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

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