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Yorodumi- PDB-1wx4: Crystal structure of the oxy-form of the copper-bound Streptomyce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wx4 | ||||||
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Title | Crystal structure of the oxy-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein prepared by the addition of dithiothreitol | ||||||
Components |
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Keywords | OXIDOREDUCTASE/METAL TRANSPORT / tyrosinase / binary complex / type-3 copper / dioxygen / 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: 1.5 Å | ||||||
Authors | Matoba, Y. / Kumagai, T. / Yamamoto, A. / Yoshitsu, H. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wx4.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wx4.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/1wx4 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/1wx4 | HTTPS FTP |
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-Related structure data
Related structure data | 1wx2C 1wx5C 1wxcSC 2ahkC 2ahlC 2zmxC 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32089.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces castaneoglobisporus (bacteria) 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) Gene: orf378 / Plasmid: pET-mel2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q83WS1 |
-Non-polymers , 4 types, 375 molecules
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-NO3 / #5: Chemical | ChemComp-PER / | #6: Water | ChemComp-HOH / | |
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-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: 33.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG3350, sodium nitrate, hepes, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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: MARRESEARCH / 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: 1.5→100 Å / Num. all: 57545 / Num. obs: 57452 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.055 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 7.7 / Num. unique all: 8285 / Rsym value: 0.189 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WXC Resolution: 1.5→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 14.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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