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- PDB-2e1m: Crystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6 -

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Basic information

Entry
Database: PDB / ID: 2e1m
TitleCrystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6
Components(L-glutamate oxidase) x 3
KeywordsOXIDOREDUCTASE / L-amino acid oxidase / L-Glutamate Oxidase / FAD / L-GOX / Flavoprotein
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
Arc Repressor Mutant, subunit A - #1620 / Arc Repressor Mutant, subunit A - #1790 / Dna Ligase; domain 1 - #470 / Double Stranded RNA Binding Domain - #490 / Alpha-Beta Plaits - #2100 / Helix Hairpins - #1210 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1500 / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / : ...Arc Repressor Mutant, subunit A - #1620 / Arc Repressor Mutant, subunit A - #1790 / Dna Ligase; domain 1 - #470 / Double Stranded RNA Binding Domain - #490 / Alpha-Beta Plaits - #2100 / Helix Hairpins - #1210 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1500 / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / : / Amine oxidase / Flavin containing amine oxidoreductase / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Double Stranded RNA Binding Domain / Dna Ligase; domain 1 / Helix non-globular / Special / FAD/NAD(P)-binding domain superfamily / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / L-glutamate oxidase precursor
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSasaki, C. / Kashima, A. / Sakaguchi, C. / Mizuno, H. / Arima, J. / Kusakabe, H. / Tamura, T. / Sugio, S. / Inagaki, K.
CitationJournal: Febs J. / Year: 2009
Title: Structural characterization of l-glutamate oxidase from Streptomyces sp. X-119-6
Authors: Arima, J. / Sasaki, C. / Sakaguchi, C. / Mizuno, H. / Tamura, T. / Kashima, A. / Kusakabe, H. / Sugio, S. / Inagaki, K.
History
DepositionOct 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,5027
Polymers76,4313
Non-polymers1,0704
Water00
1
A: L-glutamate oxidase
B: L-glutamate oxidase
C: L-glutamate oxidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)155,00314
Polymers152,8626
Non-polymers2,1418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area45710 Å2
ΔGint-259 kcal/mol
Surface area41600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.875, 123.875, 168.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein L-glutamate oxidase


Mass: 42019.227 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 15-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: X-119-6 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8L3C7, L-glutamate oxidase
#2: Protein L-glutamate oxidase


Mass: 15057.732 Da / Num. of mol.: 1 / Fragment: residues 391-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: X-119-6 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8L3C7, L-glutamate oxidase
#3: Protein L-glutamate oxidase


Mass: 19354.182 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 521-701
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: X-119-6 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8L3C7, L-glutamate oxidase
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Sequence detailsTHE PRECURSOR OF L-GLUTAMETE OXIDASE IS EXPRESSED AS ONE POLYPEPTIDE CHAIN AND MATURED BY ...THE PRECURSOR OF L-GLUTAMETE OXIDASE IS EXPRESSED AS ONE POLYPEPTIDE CHAIN AND MATURED BY PROTEOLYSIS OF ACTINASE E. WE USED THE MATURED ENZYME FOR THIS STUDY. THE MATURED ENZYME TAKES THREE CHAINS. THE N TERMINAL OF CHAIN A IS ALA15, THAT OF CHAIN B IS GLY391 AND THAT OF CHAIN C IS ALA521. BUT WE DID NOT DO THE C-TERMINAL AMINO ACID ANALYSIS UNTIL NOW.

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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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 100mM CAPS-buffer, 1200mM NaH2PO4, 800mM K2HPO4, 50mM LiSO4, 5mM DTT, 20mM KPB, 10mg/ml GOX, pH 10.50, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 1
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 22, 2004
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24388 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.043
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4.779 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F8R

1f8r


Resolution: 2.8→45.27 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2982255.12 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.308 929 4.9 %RANDOM
Rwork0.248 ---
obs0.248 19146 98.4 %-
all-19457 --
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 68 0 4807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.85 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.461 140 4.6 %
Rwork0.41 2925 -
obs--97.1 %

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