[English] 日本語
![](img/lk-miru.gif)
- PDB-3awy: Crystal structure of Streptomyces tyrosinase in a complex with ca... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3awy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Streptomyces tyrosinase in a complex with caddie M84L mutant soaked in a Cu(II)-containing solution for 80 hr | ||||||
![]() |
| ||||||
![]() | OXIDOREDUCTASE/METAL TRANSPORT / TYROSINASE / BINARY COMPLEX / TYPE-3 COPPER / DIOXYGEN / COPPER TRANSFER / OXIDOREDUCTASE-METAL TRANSPORT COMPLEX | ||||||
Function / homology | ![]() tyrosinase activity / melanin biosynthetic process / pigmentation / copper ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matoba, Y. / Sugiyama, M. | ||||||
![]() | ![]() Title: A molecular mechanism for copper transportation to tyrosinase that is assisted by a metallochaperone, caddie protein Authors: Matoba, Y. / Bando, N. / Oda, K. / Noda, M. / Higashikawa, F. / Kumagai, T. / Sugiyama, M. #1: ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 93.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3awsC ![]() 3awtC ![]() 3awuC ![]() 3awvC ![]() 3awwC ![]() 3awxC ![]() 3awzC ![]() 3ax0C ![]() 1wx2S C: citing same article ( 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.) ![]() Strain: HUT 6202 / Gene: TYRC / Plasmid: PET-MEL2 / Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 14071.605 Da / Num. of mol.: 1 / Mutation: M84L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HUT 6202 / Gene: ORF378 / Plasmid: PET-MEL2 / Production host: ![]() ![]() | ||||||
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-NO3 / #5: Water | ChemComp-HOH / | Sequence details | FOR ENTITY 1, THERE IS DIFFERENCE BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THE DEPOSITOR ...FOR ENTITY 1, THERE IS DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.32 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, SODIUM NITRATE, HEPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 3, 2010 |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→100 Å / Num. all: 47585 / Num. obs: 47585 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.8 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5 / Num. unique all: 4648 / % possible all: 99.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WX2 Resolution: 1.58→30 Å / Num. parameters: 12496 / Num. restraintsaints: 11821 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3087.73 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→30 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|