[English] 日本語
![](img/lk-miru.gif)
- PDB-7q6y: The X-ray crystal structure of CbTan2, a tannase enzyme from Clos... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7q6y | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The X-ray crystal structure of CbTan2, a tannase enzyme from Clostridium butyricum | ||||||||||||
![]() | Alpha/beta hydrolase | ||||||||||||
![]() | HYDROLASE / Tannase / Serine hydrolase / Gallate / Tannic acid | ||||||||||||
Function / homology | Alpha/Beta hydrolase fold / hydrolase activity / DI(HYDROXYETHYL)ETHER / Alpha/beta hydrolase![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Coleman, T. / Mazurkewich, S. / Larsbrink, J. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural diversity and substrate preferences of three tannase enzymes encoded by the anaerobic bacterium Clostridium butyricum. Authors: Ristinmaa, A.S. / Coleman, T. / Cesar, L. / Langborg Weinmann, A. / Mazurkewich, S. / Branden, G. / Hasani, M. / Larsbrink, J. #1: ![]() Title: The X-ray crystal structure of CbTan2, a tannase enzyme from Clostridium butyricum Authors: Coleman, T. / Mazurkewich, S. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 198 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 157.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 480.6 KB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 50.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4j0cS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 54966.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.28 % |
---|---|
Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M calcium chloride dihydrate 0.1 M sodium acetate, pH 5.0 20 % PEG 6,000 25 mg/mL protein PH range: 4.75-5.75 / Temp details: 25 C |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→46.45 Å / Num. obs: 56815 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 43.04 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 11.93 |
Reflection shell | Resolution: 2.22→2.3 Å / Redundancy: 13.5 % / Rmerge(I) obs: 2.463 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5560 / % possible all: 99.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4J0C Resolution: 2.22→46.45 Å / SU ML: 0.334 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.825 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→46.45 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|