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Yorodumi- PDB-2zmx: Crystal structure of the met1-form of the copper-bound tyrosinase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zmx | |||||||||
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Title | Crystal structure of the met1-form of the copper-bound tyrosinase in complex with a caddie protein from Streptomyces castaneoglobisporus obtained by soaking in cupric sulfate solution for 36 hours | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/METAL TRANSPORT / TYROSINASE / BINARY COMPLEX / TYPE-3 COPPER / DIOXYGEN / COPPER TRANSFER / OXIDOREDUCTASE-METAL TRANSPORT COMPLEX / Copper / Metal-binding | |||||||||
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) STREPTOMYCES CASTANEOGLOBISPORUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | |||||||||
Authors | Matoba, Y. / Sugiyama, M. | |||||||||
Citation | 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. #1: Journal: To be Published Title: X-Ray Snapshots of a Hydroxylation Mechanism of Tyrosinase Authors: Matoba, Y. / Yoshitsu, H. / Jeon, H.-J. / Oda, K. / Noda, M. / Kumagai, T. / Sugiyama, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zmx.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zmx.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 2zmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/2zmx ftp://data.pdbj.org/pub/pdb/validation_reports/zm/2zmx | HTTPS FTP |
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-Related structure data
Related structure data | 1wx2C 1wx4C 1wx5C 1wxcSC 2ahkC 2ahlC 2zn0 2zn1 2zn2 2zn3 2zn4 2zn5 2zn6 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 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: 14203.812 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*PLUS | ||||||
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-NO3 / #5: Water | ChemComp-HOH / | Sequence details | FOR THE CHAIN A, THERE IS DIFFERENCE BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THE DEPOSITOR ...FOR THE CHAIN A, THERE IS DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.44 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, SODIUM NITRATE, HEPES, pH 6.5, 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: BL41XU / Wavelength: 0.9 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→100 Å / Num. all: 79302 / Num. obs: 79302 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 43.9 |
Reflection shell | Resolution: 1.33→1.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.6 / Num. unique all: 7543 / Rsym value: 0.317 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WXC Resolution: 1.33→30 Å / Num. parameters: 13230 / Num. restraintsaints: 11927 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3266 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→30 Å
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Refine LS restraints |
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