[English] 日本語
![](img/lk-miru.gif)
- PDB-4asm: Crystal structure of the catalytic domain of beta-agarase D from ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4asm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the catalytic domain of beta-agarase D from Zobellia galactanivorans | ||||||
![]() | BETA-AGARASE D | ||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / ENDO-BETA-AGARASE | ||||||
Function / homology | ![]() beta-agarase / beta-agarase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hehemann, J.H. / Correc, G. / Bernard, T. / Michel, G. / Czjzek, M. | ||||||
![]() | ![]() Title: Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine Bacterium Zobellia Galactanivorans. Authors: Hehemann, J.H. / Correc, G. / Thomas, F. / Bernard, T. / Barbeyron, T. / Jam, M. / Helbert, W. / Michel, G. / Czjzek, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 99.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 73.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4ateC ![]() 4atfC ![]() 1o4zS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 41108.543 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 21-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-IMD / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: 28-34 % PEG 8000 AND 0,1 M IMIDAZOLE PH 8, 4% ISOPROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 3, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→56 Å / Num. obs: 55977 / % possible obs: 99.9 % / Observed criterion σ(I): 0.1 / Redundancy: 6.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 9.1 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O4Z Resolution: 1.5→56.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.134 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / 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: 13.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→56.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|