[English] 日本語
![](img/lk-miru.gif)
- PDB-5mkm: Crystal Structure of Two-Domain Laccase mutant H165F from Strepto... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5mkm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Two-Domain Laccase mutant H165F from Streptomyces griseoflavus | ||||||
![]() | Two-domain laccase | ||||||
![]() | OXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces griseoflavus | ||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gabdulkhakov, A.G. / Tishchenko, T.V. | ||||||
![]() | ![]() Title: Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase fromStreptomyces griseoflavusAc-993. Authors: Gabdulkhakov, A. / Kolyadenko, I. / Kostareva, O. / Mikhaylina, A. / Oliveira, P. / Tamagnini, P. / Lisov, A. / Tishchenko, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 330.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 266.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 520.4 KB | Display | |
Data in XML | ![]() | 58.5 KB | Display | |
Data in CIF | ![]() | 80.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fc7C ![]() 6fdjC ![]() 6rh9C ![]() 6rhqC ![]() 6s0oC ![]() 5lhlS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 34760.664 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 7 types, 304 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/O.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/O.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.12 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% PEG 6000, 0.1 M Bicine |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980583 Å / Relative weight: 1 |
Reflection | Resolution: 1.996→50 Å / Num. obs: 206927 / % possible obs: 80.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.29 % / CC1/2: 0.99 / Net I/σ(I): 5.41 |
Reflection shell | Resolution: 1.996→2.12 Å / Redundancy: 2.06 % / Mean I/σ(I) obs: 1.49 / CC1/2: 0.69 / % possible all: 78.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5LHL Resolution: 1.996→49.767 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 26.46
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.996→49.767 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|