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Yorodumi- PDB-1qal: THE ACTIVE SITE BASE CONTROLS COFACTOR REACTIVITY IN ESCHERICHIA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qal | ||||||
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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 / MUSHROOM SHAPED HOMODIMER WITH MAINLY BETA STRUCTURE. THERE ARE 3 SMALL PERIPHERAL ALPHA/BETA DOMAINS. | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Murray, J.M. / Wilmot, C.M. / Saysell, C.G. / Jaeger, J. / Knowles, P.F. / Phillips, S.E. / McPherson, M.J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: The active site base controls cofactor reactivity in Escherichia coli amine oxidase: x-ray crystallographic studies with mutational variants. Authors: Murray, J.M. / Saysell, C.G. / Wilmot, C.M. / Tambyrajah, W.S. / Jaeger, J. / Knowles, P.F. / Phillips, S.E. / 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 | 1qal.cif.gz | 325.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qal.ent.gz | 267.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/1qal ftp://data.pdbj.org/pub/pdb/validation_reports/qa/1qal | HTTPS FTP |
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-Related 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: 80784.117 Da / Num. of mol.: 2 / Mutation: D383N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Gene: MOAA / Plasmid: PKK233-3 / Production host: Escherichia coli (E. coli) / 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: 2.76 Å3/Da / Density % sol: 55.41 % | |||||||||||||||
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Crystal grow | Temperature: 315 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: VAPOR DIFFUSION, SITTING DROP, PH 7.1, 315K, 1.2 M SODIUM CITRATE, 0.1 M HEPES CRYOPROTECTANT 1.4 M SODIUM CITRATE 0.1M HEPES 20% GLYCEROL | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
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 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 1997 / 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: 2.2→20 Å / Num. all: 249774 / Num. obs: 91312 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.9 / % possible all: 84.6 |
Reflection | *PLUS |
Reflection shell | *PLUS Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Resolution: 2.2→20 Å / SU B: 6.16562 / SU ML: 0.1562 / σ(F): 0 / σ(I): 0 / ESU R: 0.28239 / ESU R Free: 0.22435 / Stereochemistry target values: ENGH & HUBER / Details: USED RESTRAINED MAXIMUM LIKELIHOOD REFINEMENT
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Solvent computation | Solvent model: RANDOM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.626 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. reflection all: 91312 / Num. reflection obs: 86197 / % reflection Rfree: 3.5 % / Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.012 |