[English] 日本語
![](img/lk-miru.gif)
- PDB-6m0w: Crystal structure of Streptococcus thermophilus Cas9 in complex w... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6m0w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Streptococcus thermophilus Cas9 in complex with the AGAA PAM | ||||||
![]() |
| ||||||
![]() | HYDROLASE/DNA/RNA / CRISPR / HYDROLASE-DNA-RNA complex | ||||||
Function / homology | ![]() maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Zhang, H. / Xu, X. / Wang, Y. / Chen, W. / Wang, Y. / Wu, Z. / Tang, N. / Wang, Y. / Zhao, S. ...Zhang, Y. / Zhang, H. / Xu, X. / Wang, Y. / Chen, W. / Wang, Y. / Wu, Z. / Tang, N. / Wang, Y. / Zhao, S. / Gan, J. / Ji, Q. | ||||||
![]() | ![]() Title: Catalytic-state structure and engineering of Streptococcus thermophilus Cas9 Authors: Zhang, Y. / Zhang, H. / Xu, X. / Wang, Y. / Chen, W. / Wang, Y. / Wu, Z. / Tang, N. / Wang, Y. / Zhao, S. / Gan, J. / Ji, Q. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 548.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 439 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 499.7 KB | Display | |
Data in XML | ![]() | 40.7 KB | Display | |
Data in CIF | ![]() | 56.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m0vC ![]() 6m0xC ![]() 5axwS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 8496.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|---|
#3: DNA chain | Mass: 2468.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-RNA chain / Protein , 2 types, 2 molecules BA
#1: RNA chain | Mass: 23227.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|---|
#4: Protein | Mass: 129646.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LMD-9 / Gene: cas9-1, csn1, STER_0709 / Production host: ![]() ![]() References: UniProt: Q03LF7, Hydrolases; Acting on ester bonds |
-Non-polymers , 2 types, 24 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.6 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: KCL, MgCL, BaCL2, MBP |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.755→50 Å / Num. obs: 43335 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.19 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Χ2: 0.794 / Net I/σ(I): 4.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5axw Resolution: 2.76→48.874 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.37
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 158.03 Å2 / Biso mean: 65.2093 Å2 / Biso min: 36.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.76→48.874 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 35.5379 Å / Origin y: 12.3075 Å / Origin z: 146.1941 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|