[English] 日本語
![](img/lk-miru.gif)
- PDB-3a4x: Crystal structures of catalytic site mutants of active domain 2 o... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3a4x | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structures of catalytic site mutants of active domain 2 of thermostable chitinase from Pyrococcus furiosus complexed with chito-oligosaccharides | |||||||||
![]() | Chitinase | |||||||||
![]() | HYDROLASE / archaea / chitinase / glycosyl hydrolase | |||||||||
Function / homology | ![]() chitinase activity / chitin catabolic process / polysaccharide binding / chitin binding / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tsuji, H. / Nishimura, S. / Inui, T. / Ishikawa, K. / Nakamura, T. / Uegaki, K. | |||||||||
![]() | ![]() Title: Kinetic and crystallographic analyses of the catalytic domain of chitinase from Pyrococcus furiosus- the role of conserved residues in the active site Authors: Tsuji, H. / Nishimura, S. / Inui, T. / Kado, Y. / Ishikawa, K. / Nakamura, T. / Uegaki, K. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 149.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 115.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 48 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a4wC ![]() 3afbC ![]() 2dskS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 34720.215 Da / Num. of mol.: 2 / Fragment: catalytic domain (AD2), UNP residues 409-717 / Mutation: D524A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 4 types, 649 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.37 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: VAPOR DIFFUSION, HANGING DROP, pH6.0, temperature 298K Temp details: 1.6M MgSO4 |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jun 2, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 88323 |
-
Processing
Software | Name: REFMAC / Version: 5.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DSK Resolution: 1.76→37.76 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.453 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.425 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→37.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.761→1.807 Å / Total num. of bins used: 20
|