[English] 日本語
Yorodumi- PDB-3l8q: Structure analysis of the type II cohesin dyad from the adaptor S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l8q | ||||||
---|---|---|---|---|---|---|---|
Title | Structure analysis of the type II cohesin dyad from the adaptor ScaA scaffoldin of Acetivibrio cellulolyticus | ||||||
Components | Cellulosomal scaffoldin adaptor protein B | ||||||
Keywords | STRUCTURAL PROTEIN / PROTEIN BINDING / Dockerin-binding module / protein-protein interactions / linker segment / scaffoldin arrangement / beta sandwich / alpha helix / beta flaps | ||||||
Function / homology | Function and homology information polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Acetivibrio cellulolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Noach, I. / Frolow, F. / Bayer, E.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Modular Arrangement of a Cellulosomal Scaffoldin Subunit Revealed from the Crystal Structure of a Cohesin Dyad Authors: Noach, I. / Levy-Assaraf, M. / Lamed, R. / Shimon, L.J.W. / Frolow, F. / Bayer, E.A. #1: Journal: J.Mol.Biol. / Year: 2009 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3l8q.cif.gz | 623.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3l8q.ent.gz | 513 KB | Display | PDB format |
PDBx/mmJSON format | 3l8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/3l8q ftp://data.pdbj.org/pub/pdb/validation_reports/l8/3l8q | HTTPS FTP |
---|
-Related structure data
Related structure data | 1zv9S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37897.426 Da / Num. of mol.: 4 / Fragment: Cohesin dyad, UNP residues 28-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: scaB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q7WYN3 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-HEZ / | #5: Water | ChemComp-HOH / | Sequence details | THE DEPOSITORS SUSPECT THAT THE ORIGINAL SEQUENCING WAS MISTAKEN AT THIS POSITION. THEIR RESULTS ...THE DEPOSITORS | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.51 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 0.15M citric acid pH 3.5, 16% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2007 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→30 Å / Num. obs: 192139 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 23.9 / Num. measured all: 707451 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8616 / Rsym value: 0.446 / % possible all: 95.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZV9 Resolution: 1.57→29.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.799 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; THE FRIEDEL PAIRS WERE USED FOR phasing.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 15.626 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.203 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→29.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.572→1.603 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|