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- PDB-6ltu: Crystal structure of Cas12i2 ternary complex with double Mg2+ bou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ltu | |||||||||
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Title | Crystal structure of Cas12i2 ternary complex with double Mg2+ bound in catalytic pocket | |||||||||
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![]() | HYDROLASE/RNA/DNA / CRISPR-Cas / Cas12i2 / Cas12i2 ternary complex / HYDROLASE / HYDROLASE-RNA-DNA complex / active RuvC state / wild type Cas12i2 / wt Cas12i2 | |||||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10)![]() | |||||||||
Biological species | unidentified (others) synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, X. / Sun, W. / Cheng, Z. / Chen, M. / Li, X. / Wang, J. / Sheng, G. / Gong, W. / Wang, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2. Authors: Huang, X. / Sun, W. / Cheng, Z. / Chen, M. / Li, X. / Wang, J. / Sheng, G. / Gong, W. / Wang, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 313.4 KB | Display | ![]() |
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PDB format | ![]() | 218.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 42.8 KB | Display | |
Data in CIF | ![]() | 62.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ltpC ![]() 6ltrSC ![]() 6lu0C 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 on special symmetry positions |
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Components
-DNA chain , 3 types, 3 molecules DCE
#3: DNA chain | Mass: 3595.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 10738.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 1464.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 121469.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) Production host: ![]() ![]() |
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#2: RNA chain | Mass: 18664.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 329 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | (1) Chain A contains the expression tag SER (0). (2) The author does not know the exact sequence of ...(1) Chain A contains the expression tag SER (0). (2) The author does not know the exact sequence of chain E. This short DNA chain is the substrate of Cas12i2 which is a DNA nuclease and it is bound in the catalytic pocket of the protein. The author built the model manually based on the Fo-Fc map and then refined the model. Due to the limited resolution, the author couldn't distinguish between DT and DC, DA and DG. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 7.2 / Details: 0.2 M NaCl, 0.1 M Tris pH 7.2, 18% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→50 Å / Num. obs: 52840 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 41.69 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.066 / Rrim(I) all: 0.174 / Χ2: 0.946 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.57→2.61 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2646 / CC1/2: 0.715 / Rpim(I) all: 0.395 / Rrim(I) all: 1.063 / Χ2: 0.847 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LTR Resolution: 2.57→46.87 Å / SU ML: 0.2979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1049 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→46.87 Å
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Refine LS restraints |
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LS refinement shell |
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