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Yorodumi- PDB-1dyu: The active site base controls cofactor reactivity in Escherichia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dyu | ||||||
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Title | The active site base controls cofactor reactivity in Escherichia coli amine oxidase: X-ray crystallographic studies with mutational variants. | ||||||
Components | COPPER AMINE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / TPQ / COPPER AMINE OXIDASE / EC 1.4.3.4 / WILDTYPE / CATALYTIC BASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Murray, J.M. / Wilmot, C.M. / Saysell, C.G. / Jaeger, J. / Knowles, P.F. / Phillips, S.E.V. / McPherson, M.J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase : X-Ray Crystallographicstudies with Mutational Variants Authors: Murray, J.M. / Wilmot, C.M. / Saysell, C.G. / Jaeger, J. / Knowles, P.F. / Phillips, S.E.V. / McPherson, M.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS ... SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS C AND C1 REPRESENT ONE BIFURCATED SHEET. SHEETS K AND K1 REPRESENT ONE BIFURCATED SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dyu.cif.gz | 326.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dyu.ent.gz | 263 KB | Display | PDB format |
PDBx/mmJSON format | 1dyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dyu ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dyu | HTTPS FTP |
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-Related structure data
Related structure data | 1qafC 1qakC 1qalC 1oacS 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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Details | BIOLOGICAL_UNIT: DIMERIC |
-Components
#1: Protein | Mass: 81366.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: EACH MONOMER CONTAINS ONE COPPER ATOM, TWO CALCIUM ATOMS, AND ONE 2,4,5, -TRIHYDROXYPHENYLALANINE QUINONE COFACTOR. Source: (gene. exp.) ESCHERICHIA COLI (E. coli) Description: CLONED AND OVER-EXPRESSED IN E. COLI USING PLASMID PKK233-3 Cellular location: PERIPLASM / Plasmid: PLASMID DERIVED FROM PKK233-3 / Cellular location (production host): PERIPLASM / 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: 55 % | |||||||||||||||
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Crystal grow | pH: 7.1 / Details: 1.2 M SODIUM CITRATE, 0.1 M HEPES PH 7.1 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||
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: ESRF / Beamline: ID2 / Wavelength: 0.99 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→20 Å / Num. obs: 105826 / % possible obs: 93.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.06 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.04→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.19 / % possible all: 91 |
Reflection | *PLUS Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 91 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OAC Resolution: 2.04→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: NEITHER THE N-TERMINAL OR C-TERMINAL AMINO ACIDS WERE WELL DEFINED BY THE ELECTRON DENSITY
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Displacement parameters | Biso mean: 31.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→20 Å
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Refine LS restraints |
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