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Yorodumi- PDB-2zwe: Crystal structure of the copper-bound tyrosinase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zwe | ||||||
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Title | Crystal structure of the copper-bound tyrosinase in complex with a caddie protein from streptomyces castaneoglobisporus obtained by soaking the deoxy-form crystal in dioxygen-saturated solution for 40 minutes | ||||||
Components |
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Keywords | OXIDOREDUCTASE/METAL TRANSPORT / TYROSINASE / BINARY COMPLEX / TYPE-3 COPPER / DIOXYGEN / COPPER TRANSFER / OXIDOREDUCTASE-METAL TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information melanin biosynthetic process / oxidoreductase activity / copper ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces castaneoglobisporus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Matoba, Y. / Sugiyama, M. | ||||||
Citation | Journal: To be Published Title: Crystallographic evidence of drastic movement of a copper ion toward the substrate tyrosine for starting hydroxylation reaction of tyrosinase Authors: Matoba, Y. / Yoshitsu, H. / Jeon, H.J. / Oda, K. / Noda, M. / Kumagai, T. / Sugiyama, M. #1: Journal: J.Biol.Chem. / Year: 2006 Title: Crystallographic evidence that the dinuclear copper center of tyrosinase is flexible during catalysis Authors: Matoba, Y. / Kumagai, T. / Yamamoto, A. / Yoshitsu, H. / Sugiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zwe.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zwe.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zwe ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zwe | HTTPS FTP |
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-Related structure data
Related structure data | 2zwdC 2zwfC 2zwgC 1wx3 2zwc C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32089.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria) Strain: HUT 6202 / Gene: TYRC / Plasmid: PET-MEL2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q83WS2, tyrosinase | ||||||
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#2: Protein | Mass: 14219.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria) Strain: HUT 6202 / Gene: ORF378 / Plasmid: PET-MEL2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q83WS1 | ||||||
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-NO3 / #5: Water | ChemComp-HOH / | Sequence details | THOUGH DAH IS DEFINED AS A MODIFIED PHE, IT IS ALSO A MODIFIED TYR IN THIS ENTRY. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 35.25 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, SODIUM NITRATE, HEPES, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→100 Å / Num. all: 82482 / Num. obs: 82482 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 1.32→1.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.2 / Num. unique all: 8236 / Rsym value: 0.303 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WX3 1wx3 Resolution: 1.32→30 Å / Num. parameters: 13335 / Num. restraintsaints: 12024 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3273.79 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→30 Å
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Refine LS restraints |
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