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Yorodumi- PDB-2wgq: Zinc substituted E Coli Copper Amine Oxidase, a model for the pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wgq | ||||||
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Title | Zinc substituted E Coli Copper Amine Oxidase, a model for the precursor for 2,4,5-trihydroxyphenylalaninequinone formation | ||||||
Components | AMINE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / TPQ / ZINC / COPPER / CALCIUM / PERIPLASM / AMINE OXIDASE / METAL-BINDING | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Moody, P.C.E. / Cooper, R.A. | ||||||
Citation | Journal: To be Published Title: The Structure of E Coli Amine Oxidase with the Cataltyic Copper Subsituted for Zinc - a Model Precursor. Authors: Moody, P.C.E. / Cooper, R.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wgq.cif.gz | 294.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wgq.ent.gz | 239.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wgq_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 2wgq_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 2wgq_validation.xml.gz | 55.3 KB | Display | |
Data in CIF | 2wgq_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wgq ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wgq | HTTPS FTP |
-Related structure data
Related structure data | 1spuS 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: 81336.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P46883, EC: 1.4.3.6 #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: 2.69 Å3/Da / Density % sol: 53.96 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 27.3 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SPU Resolution: 2.5→39.72 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / SU B: 10.262 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.659 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL REFINEMENT WITH CNS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.338 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→39.72 Å
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Refine LS restraints |
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