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- PDB-6m0v: Crsytal structure of streptococcus thermophilus Cas9 in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m0v | ||||||
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Title | Crsytal structure of streptococcus thermophilus Cas9 in complex with the GGAA PAM | ||||||
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![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 284.4 KB | Display | ![]() |
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PDB format | ![]() | 215.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473 KB | Display | ![]() |
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Full document | ![]() | 487.3 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m0wC ![]() 6m0xC ![]() 5axwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 8481.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 2484.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-RNA chain / Protein , 2 types, 2 molecules BA
#1: RNA chain | Mass: 22882.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#4: Protein | Mass: 129646.898 Da / Num. of mol.: 1 / Mutation: H599A 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 , 3 types, 20 molecules ![](data/chem/img/BA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-BA / #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.44 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: KCL, MgCl2, MPD, MgCl2 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 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: 3→50 Å / Num. obs: 31477 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.43 Å2 / CC1/2: 0.8 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 3→3.11 Å / Num. unique obs: 1824 / CC1/2: 0.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5axw Resolution: 3→48.822 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.71 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 245.41 Å2 / Biso mean: 53.4285 Å2 / Biso min: 16.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→48.822 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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