[English] 日本語
![](img/lk-miru.gif)
- PDB-2xdh: Non-cellulosomal cohesin from the hyperthermophilic archaeon Arch... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2xdh | ||||||
---|---|---|---|---|---|---|---|
Title | Non-cellulosomal cohesin from the hyperthermophilic archaeon Archaeoglobus fulgidus | ||||||
![]() | COHESIN | ||||||
![]() | CELL ADHESION / ARCHAEAL PROTEIN | ||||||
Function / homology | ![]() polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Voronov-Goldman, M. / Lamed, R. / Noach, I. / Borovok, I. / Kwiat, M. / Rosenheck, S. / Shimon, L.J.W. / Bayer, E.A. / Frolow, F. | ||||||
![]() | ![]() Title: Non-Cellulosomal Cohesin from the Hyperthermophilic Archaeon Archaeoglobus Fulgidus Authors: Voronov-Goldman, M. / Lamed, R. / Noach, I. / Borovok, I. / Kwiat, M. / Rosenheck, S. / Shimon, L.J.W. / Bayer, E.A. / Frolow, F. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and Preliminary X-Ray Analysis of a Cohesin-Like Module from Af2375 of the Archaeon Archaeoglobus Fulgidus. Authors: Voronov-Goldman, M. / Noach, I. / Lamed, R. / Shimon, L.J.W. / Borovok, I. / Bayer, E.A. / Frolow, F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1anuS ![]() 1aohS ![]() 1g1kS ![]() 1qznS ![]() 1tyjS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 17635.570 Da / Num. of mol.: 1 / Fragment: ORF 2375, RESIDUES 278-433 Source method: isolated from a genetically manipulated source Details: COHESIN MODULE OF ORF 2375 / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.53 % / Description: NONE |
---|---|
Crystal grow | Details: 0.1 M TRIS HYDROCHLORIDE PH 8.5, 2 M MONO-AMMONIUM DIHYDROGEN PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. obs: 13584 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 18.5 % / Biso Wilson estimate: 37.67 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 46.6 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1ANU, 1AOH, 1G1K, 1QZN, 1TYJ Resolution: 1.96→25.438 Å / SU ML: 0.26 / σ(F): 0.05 / Phase error: 20.89 / Stereochemistry target values: ML / Details: DISORDERED REGION A97-A123 IS OMITTED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.152 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→25.438 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 51.3317 Å / Origin y: 80.8691 Å / Origin z: 36.0372 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: CHAIN A |