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Yorodumi- PDB-6kc7: Crystal structure of Nme1Cas9 in complex with sgRNA and target DN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kc7 | ||||||
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Title | Crystal structure of Nme1Cas9 in complex with sgRNA and target DNA (ATATGATT PAM) in seed-base paring state | ||||||
Components |
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Keywords | HYDROLASE/RNA/DNA / CRISPR-Cas9 / NmeCas9 / Nme1Cas9 / hydrolase / ternary complex / HYDROLASE-RNA-DNA 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: 3.3 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 | 6kc7.cif.gz | 285.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kc7.ent.gz | 214.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kc7_validation.pdf.gz | 478.5 KB | Display | wwPDB validaton report |
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Full document | 6kc7_full_validation.pdf.gz | 518.2 KB | Display | |
Data in XML | 6kc7_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 6kc7_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kc7 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kc7 | HTTPS FTP |
-Related structure data
Related structure data | 6jdqSC 6jdvC 6je3C 6je4C 6je9C 6jfuC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 124633.898 Da / Num. of mol.: 1 / Mutation: H588A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Gene: cas9, NMV_1993 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: C9X1G5, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 43059.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 5850.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TS8 target DNA / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 3362.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: non-target DNA strand / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.26 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 8 Details: 0.2M Na nitrate, 0.1M Bis-Tris propane pH 8.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 28597 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.053 / Rrim(I) all: 0.11 / Χ2: 0.922 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2824 / CC1/2: 0.991 / Rpim(I) all: 0.516 / Rrim(I) all: 1.048 / Χ2: 1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JDQ Resolution: 3.3→46.2 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→46.2 Å
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Refine LS restraints |
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LS refinement shell |
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