[English] 日本語
Yorodumi- PDB-3oq2: Structure of a CRISPR associated protein Cas2 from Desulfovibrio ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oq2 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a CRISPR associated protein Cas2 from Desulfovibrio vulgaris | ||||||
Components | CRISPR-associated protein Cas2 | ||||||
Keywords | IMMUNE SYSTEM / Ferredoxin fold / CRISPR | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Samai, P. / Smith, P. / Shuman, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris. Authors: Samai, P. / Smith, P. / Shuman, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3oq2.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3oq2.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oq2 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oq2 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 11946.675 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / Gene: cas2, DVUA0135 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72WF4 |
---|
-Non-polymers , 6 types, 329 molecules
#2: Chemical | ChemComp-NA / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-TRS / | ||||
#4: Chemical | ChemComp-CL / | ||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Protein solution 0.85 mM DvuCas2, reservoir solution 1 M lithium sulfate, 0.5 M ammonium sulfate and 0.1 M trisodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 130 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 46959 / Num. obs: 45550 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.049 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.35→50 Å / % possible all: 97 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.35→29.079 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 15.33 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.4 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.873 Å2 / ksol: 0.446 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→29.079 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|