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Yorodumi- PDB-7d3j: Crystal structure of the Cas12i1 R-loop complex after target DNA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d3j | ||||||
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Title | Crystal structure of the Cas12i1 R-loop complex after target DNA cleavage | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / The RNP Complex 2 | ||||||
Function / homology | CITRIC ACID / DNA / DNA (> 10) / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Lachnospiraceae bacterium ND2006 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Zhang, B. / Luo, D.Y. / Li, Y. / OuYang, S.Y. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1. Authors: Zhang, B. / Luo, D. / Li, Y. / Perculija, V. / Chen, J. / Lin, J. / Ye, Y. / Ouyang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d3j.cif.gz | 285.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d3j.ent.gz | 219.7 KB | Display | PDB format |
PDBx/mmJSON format | 7d3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/7d3j ftp://data.pdbj.org/pub/pdb/validation_reports/d3/7d3j | HTTPS FTP |
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-Related structure data
Related structure data | 7d2lSC 7d8cC 7eu9C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules CD
#3: DNA chain | Mass: 12326.935 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria) |
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#4: DNA chain | Mass: 12257.882 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria) |
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 126950.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria) Production host: Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 13781.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria) Production host: Escherichia coli (E. coli) |
-Non-polymers , 2 types, 41 molecules
#5: Chemical | ChemComp-CIT / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.59 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate (pH 5.4), 15% (w/v) Polyethylene glycol 3350, 0.2 M lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→58.73 Å / Num. obs: 70800 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.45→2.51 Å / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4504 / CC1/2: 0.901 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D2L Resolution: 2.45→58.73 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 192.13 Å2 / Biso mean: 61.968 Å2 / Biso min: 25.95 Å2
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Refinement step | Cycle: final / Resolution: 2.45→58.73 Å
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LS refinement shell | Resolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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