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Yorodumi- PDB-1f8s: CRYSTAL STRUCTURE OF L-AMINO ACID OXIDASE FROM CALLOSELASMA RHODO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f8s | |||||||||
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Title | CRYSTAL STRUCTURE OF L-AMINO ACID OXIDASE FROM CALLOSELASMA RHODOSTOMA, COMPLEXED WITH THREE MOLECULES OF O-AMINOBENZOATE. | |||||||||
Components | L-AMINO ACID OXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / OXIDASE / ENANTIOMERIC SPECIFICITY / o-AMINOBENZOATE / ACTIVE SITE FUNNEL / HELICAL DOMAIN / FAD-BINDING DOMAIN | |||||||||
Function / homology | Function and homology information L-phenylalaine oxidase activity / L-amino-acid oxidase / toxin activity / killing of cells of another organism / defense response to bacterium / apoptotic process / extracellular region Similarity search - Function | |||||||||
Biological species | Calloselasma rhodostoma (Malayan pit viper) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | |||||||||
Authors | Pawelek, P.D. / Cheah, J. / Coulombe, R. / Macheroux, P. / Ghisla, S. / Vrielink, A. | |||||||||
Citation | Journal: EMBO J. / Year: 2000 Title: The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site. Authors: Pawelek, P.D. / Cheah, J. / Coulombe, R. / Macheroux, P. / Ghisla, S. / Vrielink, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f8s.cif.gz | 818.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f8s.ent.gz | 673.5 KB | Display | PDB format |
PDBx/mmJSON format | 1f8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/1f8s ftp://data.pdbj.org/pub/pdb/validation_reports/f8/1f8s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Details | Biological unit is a dimer. |
-Components
#1: Protein | Mass: 56299.258 Da / Num. of mol.: 8 / Source method: isolated from a natural source Source: (natural) Calloselasma rhodostoma (Malayan pit viper) Secretion: VENOM / References: UniProt: P81382, L-amino-acid oxidase #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-BE2 / #4: Chemical | ChemComp-FAD / #5: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG4000, ammonium sulfate, sodium citrate, glycerol, o-aminobenzoate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal grow | *PLUS Details: Jancarik, J., (1991) J. Appl. Crystallogr., 24, 409. |
Components of the solutions | *PLUS Conc.: 10 mg/ml / Common name: protein |
-Data collection
Diffraction | Mean temperature: 83 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 31, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 395029 / Num. obs: 335974 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 1.13 % / Rmerge(I) obs: 0.378 / Num. unique all: 12419 / % possible all: 47.4 |
-Processing
Software |
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Refinement | Resolution: 2→500 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 3864620.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: HIS223 IN CHAINS A-H WERE MODELLED AND REFINED WITH TWO ALTERNATE CONFORMATIONS EACH HAVING HALF OCCUPANCY F0-FC DENSITY OBSERVED EXTENDING FROM ALA149 SUGGESTING POSSIBLE SEQUENCING ERROR
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.32 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→500 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.267 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.241 |