+Open data
-Basic information
Entry | Database: PDB / ID: 7c3h | |||||||||
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Title | Structure of L-lysine oxidase in complex with L-lysine | |||||||||
Components | L-lysine oxidase | |||||||||
Keywords | OXIDOREDUCTASE / L-amino acid oxidase | |||||||||
Function / homology | Function and homology information L-lysine oxidase / L-lysine oxidase activity / L-amino-acid oxidase activity / amino acid catabolic process / nucleotide binding Similarity search - Function | |||||||||
Biological species | Hypocrea rufa (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Kondo, H. / Kitagawa, M. / Sugiyama, S. / Imada, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Structural basis of strict substrate recognition of l-lysine alpha-oxidase from Trichoderma viride. Authors: Kondo, H. / Kitagawa, M. / Matsumoto, Y. / Saito, M. / Amano, M. / Sugiyama, S. / Tamura, T. / Kusakabe, H. / Inagaki, K. / Imada, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c3h.cif.gz | 294 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c3h.ent.gz | 188.9 KB | Display | PDB format |
PDBx/mmJSON format | 7c3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c3h_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7c3h_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7c3h_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 7c3h_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/7c3h ftp://data.pdbj.org/pub/pdb/validation_reports/c3/7c3h | HTTPS FTP |
-Related structure data
Related structure data | 7c3iC 7c3jC 7c3lC 3x0vS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60875.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea rufa (fungus) / Strain: Y244-2 / Production host: Streptomyces lividans TK24 (bacteria) References: UniProt: A0A0J9X1X3, UniProt: A0A0G4DCU0*PLUS, L-lysine oxidase |
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-Non-polymers , 5 types, 928 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / pH: 7 Details: 4% (w/v) PEG 400, 0.1 M HEPES pH 7.0, 2.0 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 22, 2014 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24 Å / Num. obs: 129154 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 12.33 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 18744 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X0V Resolution: 1.7→23.98 Å / SU ML: 0.1615 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0501 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→23.98 Å
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Refine LS restraints |
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LS refinement shell |
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