[English] 日本語
Yorodumi- PDB-2zwd: Crystal structure of the copper-bound tyrosinase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zwd | ||||||
---|---|---|---|---|---|---|---|
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 5 minutes | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE/METAL TRANSPORT / TYROSINASE / BINARY COMPLEX / TYPE-3 COPPER / DIOXYGEN / COPPER TRANSFER / OXIDOREDUCTASE-METAL TRANSPORT COMPLEX | ||||||
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: 1.35 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zwd.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zwd.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zwd_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2zwd_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 2zwd_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 2zwd_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zwd ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zwd | HTTPS FTP |
-Related structure data
Related structure data | 2zweC 2zwfC 2zwgC 1wx3 2zwc C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q83WS2, tyrosinase | ||||
---|---|---|---|---|---|
#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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q83WS1 | ||||
#3: Chemical | ChemComp-CU1 / #4: Chemical | ChemComp-NO3 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.19 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→100 Å / Num. all: 77848 / Num. obs: 77848 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 38 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4 / Num. unique all: 7668 / Rsym value: 0.32 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WX3 1wx3 Resolution: 1.35→30 Å / Num. parameters: 13276 / Num. restraintsaints: 11922 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3233.9 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→30 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|