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Yorodumi- PDB-2e1m: Crystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e1m | ||||||
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Title | Crystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6 | ||||||
Components | (L-glutamate oxidase) x 3 | ||||||
Keywords | OXIDOREDUCTASE / 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 | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Sasaki, C. / Kashima, A. / Sakaguchi, C. / Mizuno, H. / Arima, J. / Kusakabe, H. / Tamura, T. / Sugio, S. / Inagaki, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e1m.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e1m.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 2e1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e1m_validation.pdf.gz | 739.4 KB | Display | wwPDB validaton report |
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Full document | 2e1m_full_validation.pdf.gz | 763.4 KB | Display | |
Data in XML | 2e1m_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 2e1m_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/2e1m ftp://data.pdbj.org/pub/pdb/validation_reports/e1/2e1m | HTTPS FTP |
-Related structure data
Related structure data | 1f8rS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | ||||
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#2: Protein | 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 | 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 | #5: Chemical | ChemComp-FAD / | Sequence details | THE PRECURSOR OF L-GLUTAMETE OXIDASE IS EXPRESSED AS ONE POLYPEPTIDE CHAIN AND MATURED BY ...THE PRECURSOR OF L-GLUTAMETE OXIDASE IS EXPRESSED AS ONE POLYPEPTID | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 1 |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 22, 2004 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.6→2.69 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4.779 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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
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Displacement parameters | Biso mean: 34.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→45.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.85 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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