+Open data
-Basic information
Entry | Database: PDB / ID: 5de0 | ||||||
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Title | Dye-decolorizing protein from V. cholerae | ||||||
Components | Deferrochelatase | ||||||
Keywords | OXIDOREDUCTASE / heme complex | ||||||
Function / homology | Function and homology information melanin metabolic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / cytosol Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Uchida, T. / Sasaki, M. / Tanaka, Y. / Yao, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochemistry / Year: 2015 Title: A Dye-Decolorizing Peroxidase from Vibrio cholerae. Authors: Uchida, T. / Sasaki, M. / Tanaka, Y. / Ishimori, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5de0.cif.gz | 247.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5de0.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 5de0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5de0_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5de0_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5de0_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 5de0_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/5de0 ftp://data.pdbj.org/pub/pdb/validation_reports/de/5de0 | HTTPS FTP |
-Related structure data
Related structure data | 3qnrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33829.387 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: DN30_2082, VC39_07860, VC78_07860, VS27_03965, WG08_01515 Production host: Escherichia coli (E. coli) / References: UniProt: A0A085T8S6, UniProt: Q9KQ59*PLUS #2: Chemical | ChemComp-HEM / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: potassium thiocyanate, PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 50860 / % possible obs: 99.8 % / Redundancy: 5.83 % / Rsym value: 0.12 / Net I/σ(I): 12.51 |
Reflection shell | Resolution: 2.24→2.38 Å / Redundancy: 5.72 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.4 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QNR Resolution: 2.24→41.296 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→41.296 Å
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Refine LS restraints |
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LS refinement shell |
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