[English] 日本語
![](img/lk-miru.gif)
- PDB-3ghp: Structure of the second type II cohesin module from the adaptor S... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ghp | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the second type II cohesin module from the adaptor ScaA scaffoldin of Acetivibrio cellulolyticus (including long C-terminal linker) | ||||||
![]() | Cellulosomal scaffoldin adaptor protein B | ||||||
![]() | STRUCTURAL PROTEIN / Linker segments / beta barrel / alpha helix / beta flaps | ||||||
Function / homology | ![]() polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Noach, I. / Frolow, F. / Bayer, E.A. | ||||||
![]() | ![]() Title: Intermodular linker flexibility revealed from crystal structures of adjacent cellulosomal cohesins of Acetivibrio cellulolyticus Authors: Noach, I. / Frolow, F. / Alber, O. / Lamed, R. / Shimon, L.J.W. / Bayer, E.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization and preliminary X-ray analysis of Acetivibrio cellulolyticus cellulosomal type II cohesin module: two versions having different linker lengths Authors: Noach, I. / Alber, O. / Bayer, E.A. / Lamed, R. / Levy-Assaraf, M. / Shimon, L.J.W. / Frolow, F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 160.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 127.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 478 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zv9C ![]() 3bwzC ![]() 3fnkSC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 24484.543 Da / Num. of mol.: 2 / Fragment: Cohesin module residues 190-408 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.23 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 10%(v/v) 2-propanol, 17%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2006 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.487→50 Å / Num. all: 12802 / Num. obs: 12802 / % possible obs: 71.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 64.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.487→2.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.1 / Num. unique all: 211 / Rsym value: 0.377 / % possible all: 24.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB entry 3FNK Resolution: 2.487→42.601 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 2.08 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 37.21 / Stereochemistry target values: ML Details: Refinement made using Refmac 5.5.0066. For the last refinement cycles Phenix was used.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.251 Å2 / ksol: 0.301 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 206.01 Å2 / Biso mean: 71.096 Å2 / Biso min: 23.09 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.41 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.487→42.601 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Details: all / Origin x: 4.0121 Å / Origin y: -31.0123 Å / Origin z: 13.896 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |