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Yorodumi- PDB-1qaf: THE ACTIVE SITE BASE CONTROLS COFACTOR REACTIVITY IN ESCHERICHIA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qaf | ||||||
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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 | PROTEIN (COPPER AMINE OXIDASE) | ||||||
Keywords | OXIDOREDUCTASE / CATALYTIC DOMAIN MAINLY ANTI-PARALLEL BETA SHEET / THREE PERIPHERAL ALPHA-BETA DOMAINS | ||||||
Function / homology | Function and homology information phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / 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: 2.2 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 | 1qaf.cif.gz | 330.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qaf.ent.gz | 260.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qaf_validation.pdf.gz | 474.9 KB | Display | wwPDB validaton report |
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Full document | 1qaf_full_validation.pdf.gz | 548.2 KB | Display | |
Data in XML | 1qaf_validation.xml.gz | 75 KB | Display | |
Data in CIF | 1qaf_validation.cif.gz | 109.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/1qaf ftp://data.pdbj.org/pub/pdb/validation_reports/qa/1qaf | HTTPS FTP |
-Related structure data
Related structure data | 1dyuC 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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-Components
#1: Protein | Mass: 80799.125 Da / Num. of mol.: 2 / Mutation: D383E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Description: ESCHERICHIA COLI PERIPLASM / Cellular location: PERIPLASM / Gene: maoA / Plasmid: PKK233-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P46883, monoamine oxidase #2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / | #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: 2.79 Å3/Da / Density % sol: 55.92 % | |||||||||||||||
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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, 315 K SODIUM CITRATE, HEPES | |||||||||||||||
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: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 21, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 92396 / Num. obs: 92396 / % possible obs: 91.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.03 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.2 / % possible all: 73.3 |
Reflection | *PLUS Num. obs: 84390 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1OAC Resolution: 2.2→20 Å / SU B: 6.16638 / SU ML: 0.15259 / σ(F): 0 / σ(I): 0 / ESU R: 0.27486 / ESU R Free: 0.22699 / Stereochemistry target values: ENGH & HUBER / Details: USED SIGMA A WEIGHTED MAXIMUM LIKELIHOOD TARGETS.
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Displacement parameters | Biso mean: 32.227 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: 92396 / Num. reflection obs: 82076 / % reflection Rfree: 3.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |