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Yorodumi- PDB-6je4: Crystal structure of Nme1Cas9-sgRNA-dsDNA dimer mediated by doubl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6je4 | ||||||
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Title | Crystal structure of Nme1Cas9-sgRNA-dsDNA dimer mediated by double protein inhibitor AcrIIC3 monomers | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR/DNA/RNA / CRISPR-Cas9 / NmeCas9 / Nme1Cas9 / AcrIIC3 / anti-CRISPR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR-DNA-RNA complex | ||||||
Function / homology | Function and homology information 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 | Neisseria meningitidis 8013 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.069 Å | ||||||
Authors | Sun, W. / Yang, J. / Cheng, Z. / Liu, C. / Wang, K. / Huang, X. / Wang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol.Cell / Year: 2019 Title: Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States. Authors: Sun, W. / Yang, J. / Cheng, Z. / Amrani, N. / Liu, C. / Wang, K. / Ibraheim, R. / Edraki, A. / Huang, X. / Wang, M. / Wang, J. / Liu, L. / Sheng, G. / Yang, Y. / Lou, J. / Sontheimer, E.J. / Wang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6je4.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6je4.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6je4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6je4_validation.pdf.gz | 629.5 KB | Display | wwPDB validaton report |
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Full document | 6je4_full_validation.pdf.gz | 735.2 KB | Display | |
Data in XML | 6je4_validation.xml.gz | 180.3 KB | Display | |
Data in CIF | 6je4_validation.cif.gz | 250.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/6je4 ftp://data.pdbj.org/pub/pdb/validation_reports/je/6je4 | HTTPS FTP |
-Related structure data
Related structure data | 6jdqSC 6jdvC 6je3C 6je9C 6jfuC 6kc7C 6kc8C 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules AEKOIJST
#1: Protein | Mass: 124589.883 Da / Num. of mol.: 4 / Mutation: D16A,H588A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Strain: 8013 / Gene: cas9, NMV_1993 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: C9X1G5, Hydrolases; Acting on ester bonds #5: Protein | Mass: 13457.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Strain: 8013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E2QDI5, UniProt: A0A425B395*PLUS |
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-DNA chain , 2 types, 8 molecules CGMQDHNR
#2: DNA chain | Mass: 10836.049 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 10858.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-RNA chain , 1 types, 4 molecules BFLP
#4: RNA chain | Mass: 43059.352 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 84 molecules
#6: Chemical | ChemComp-EDO / #7: Chemical | #8: Water | ChemComp-HOH / | |
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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: 3.04 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 5.8 Details: 1M NaCl, 0.1M citric pH 5.76, 30% PEG 600, 9.6% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.06 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→50 Å / Num. obs: 178199 / % possible obs: 98.5 % / Redundancy: 4.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.069 / Rrim(I) all: 0.15 / Χ2: 0.925 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.06→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8728 / CC1/2: 0.508 / Rpim(I) all: 0.384 / Rrim(I) all: 0.804 / Χ2: 0.802 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JDQ Resolution: 3.069→46.284 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.069→46.284 Å
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Refine LS restraints |
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LS refinement shell |
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