+Open data
-Basic information
Entry | Database: PDB / ID: 6jdq | ||||||
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Title | Crystal structure of Nme1Cas9 in complex with sgRNA | ||||||
Components |
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Keywords | HYDROLASE/RNA / CRISPR-Cas9 / NmeCas9 / binary / Nme1Cas9 / hydrolase / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis serogroup C (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 | 6jdq.cif.gz | 290.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jdq.ent.gz | 222.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/6jdq ftp://data.pdbj.org/pub/pdb/validation_reports/jd/6jdq | HTTPS FTP |
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-Related structure data
Related structure data | 6jdvSC 6je3C 6je4C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 125935.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup C (strain 8013) (bacteria) Strain: 8013 / 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.43 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 8.5 / Details: 0.1M tris pH 8.5, 0.12M K2SO4, 18.5% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 45932 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Χ2: 0.949 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2270 / CC1/2: 0.619 / Rpim(I) all: 0.455 / Χ2: 0.855 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JDV Resolution: 2.95→48.914 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→48.914 Å
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Refine LS restraints |
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LS refinement shell |
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