[English] 日本語
![](img/lk-miru.gif)
- PDB-1k42: The Solution Structure of the CBM4-2 Carbohydrate Binding Module ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1k42 | ||||||
---|---|---|---|---|---|---|---|
Title | The Solution Structure of the CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase. | ||||||
![]() | Xylanase | ||||||
![]() | HYDROLASE / beta-sandwich formed by 11 strands. Binding-site cleft. Solvent exposed aromatics (Trp69 / Phe110) in binding cleft. Two helical twists. Two calcium binding sites. | ||||||
Function / homology | ![]() xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / hybrid distance geometry, simulated annealing using XPLOR | ||||||
![]() | Simpson, P.J. / Jamieson, S.J. / Abou-Hachem, M. / Nordberg-Karlsson, E. / Gilbert, H.J. / Holst, O. / Williamson, M.P. | ||||||
![]() | ![]() Title: The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase. Authors: Simpson, P.J. / Jamieson, S.J. / Abou-Hachem, M. / Karlsson, E.N. / Gilbert, H.J. / Holst, O. / Williamson, M.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 582.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 484.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 346.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 509.1 KB | Display | |
Data in XML | ![]() | 67.4 KB | Display | |
Data in CIF | ![]() | 89.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: Protein | Mass: 18103.803 Da / Num. of mol.: 1 Fragment: Second family 4 carbohydrate binding module (CBM4-2)(Residues 211-373) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-
Sample preparation
Details | Contents: 1.5 mM CBM4-2 15N-labelled, and 13C,15N double labelled protein; 50 mM CaCl2, 50 mM sodium acetate-d3, pH 6.0, 10% D2O, 10 mM sodium azide, 0.1 mM sodium trimethylsilylpropionate (TSP) Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 0.2 M / pH: 6.0 / Pressure: ambient / Temperature: 310 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
|
-
Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: hybrid distance geometry, simulated annealing using XPLOR Software ordinal: 1 Details: The final set of restraints contained 1654 non-redundant unambiguous NOEs and 17 ambiguous NOEs, 93 dihedral angle restraints, 72 chi1 and 1 chi2 restraint, and 65 pairs of hydrogen bond ...Details: The final set of restraints contained 1654 non-redundant unambiguous NOEs and 17 ambiguous NOEs, 93 dihedral angle restraints, 72 chi1 and 1 chi2 restraint, and 65 pairs of hydrogen bond restraints, plus 177 backbone dihedral restraints based on 13C shifts from TALOS. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 12 |