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Yorodumi- PDB-2zwn: Crystal structure of the novel two-domain type laccase from a met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zwn | ||||||
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Title | Crystal structure of the novel two-domain type laccase from a metagenome | ||||||
Components | two-domain type laccase | ||||||
Keywords | OXIDOREDUCTASE / laccase / Muticopper oxidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | metagenomes (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Komori, H. / Miyazaki, K. / Higuchi, Y. | ||||||
Citation | Journal: Febs Lett. / Year: 2009 Title: X-ray structure of a two-domain type laccase: a missing link in the evolution of multi-copper proteins Authors: Komori, H. / Miyazaki, K. / Higuchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zwn.cif.gz | 207.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zwn.ent.gz | 165.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zwn ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zwn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38194.895 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenomes (others) / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / References: UniProt: C0STU6*PLUS #2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. | |
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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: 2.04 Å3/Da / Density % sol: 39.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Potassium chloride, 0.05M HEPES, pH7.5, 35% Pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.01 Å / Num. obs: 98106 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→35.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.139 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.177 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→35.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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