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Yorodumi- PDB-1jrq: X-ray Structure Analysis of the Role of the Conserved Tyrosine-36... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jrq | ||||||
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Title | X-ray Structure Analysis of the Role of the Conserved Tyrosine-369 in Active Site of E. coli Amine Oxidase | ||||||
Components | Copper amine oxidase | ||||||
Keywords | OXIDOREDUCTASE / Copper amine oxidase / TPQ / mutant | ||||||
Function / homology | Function and homology information phenylethylamine catabolic process / primary amine oxidase activity / : / : / : / primary-amine oxidase / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space ...phenylethylamine catabolic process / primary amine oxidase activity / : / : / : / primary-amine oxidase / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.15 Å | ||||||
Authors | Murray, J.M. / Kurtis, C.R. / Tambarajah, W. / Saysell, C.G. / Wilmot, C.M. / Parsons, M.R. / Phillips, S.E.V. / Knowles, P.F. / McPherson, M.J. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Conserved tyrosine-369 in the active site of Escherichia coli copper amine oxidase is not essential. Authors: Murray, J.M. / Kurtis, C.R. / Tambyrajah, W. / Saysell, C.G. / Wilmot, C.M. / Parsons, M.R. / Phillips, S.E. / Knowles, P.F. / McPherson, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jrq.cif.gz | 323.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jrq.ent.gz | 259 KB | Display | PDB format |
PDBx/mmJSON format | 1jrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jrq ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jrq | HTTPS FTP |
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-Related structure data
Related structure data | 1oacS 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: 81350.727 Da / Num. of mol.: 2 / Mutation: Y369F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5a / Cellular location: PERIPLASM / Plasmid: pKK233 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P46883, monoamine oxidase #2: Chemical | #3: Chemical | ChemComp-CA / #4: 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: 2.73 Å3/Da / Density % sol: 54.94 % | |||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: SODIUM CITRATE, HEPES BUFFER, pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 291K | |||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9 / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 1999 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 110510 / % possible obs: 91.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.7 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.336 / % possible all: 87 |
Reflection | *PLUS Num. obs: 90148 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Rmerge(I) obs: 0.336 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1OAC Resolution: 2.15→20 Å / σ(F): 0
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Displacement parameters | Biso mean: 35.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.1 Å / Total num. of bins used: 10 / % reflection obs: 91.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 87056 / σ(F): 0 / Num. reflection Rfree: 3092 / % reflection Rfree: 3.5 % / Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: o_bond_d / Dev ideal: 0.01 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å |