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Yorodumi- PDB-2zmy: Crystal structure of the met2-form of the copper-bound tyrosinase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zmy | ||||||
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Title | Crystal structure of the met2-form of the copper-bound tyrosinase in complex with a caddie protein from Streptomyces castaneoglobisporus obtained by soaking in cupric sulfate solution for 80 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 tyrosinase activity / melanin biosynthetic process / pigmentation / copper ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES CASTANEOGLOBISPORUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Matoba, Y. / Sugiyama, M. | ||||||
Citation | 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. #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 | 2zmy.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zmy.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zmy_validation.pdf.gz | 447.3 KB | Display | wwPDB validaton report |
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Full document | 2zmy_full_validation.pdf.gz | 452.2 KB | Display | |
Data in XML | 2zmy_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 2zmy_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/2zmy ftp://data.pdbj.org/pub/pdb/validation_reports/zm/2zmy | HTTPS FTP |
-Related structure data
Related structure data | 2zmzC 1wx3 2zn0 2zn1 2zn2 2zn3 2zn4 2zn5 2zn6 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: 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: 1.85 Å3/Da / Density % sol: 34.39 % |
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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: BL38B1 / Wavelength: 0.8 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→100 Å / Num. all: 62449 / Num. obs: 62449 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6161 / Rsym value: 0.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WX3 1wx3 Resolution: 1.45→30 Å / Num. parameters: 13136 / Num. restraintsaints: 12026 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3237 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→30 Å
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Refine LS restraints |
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