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Yorodumi- PDB-6jdj: Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jdj | ||||||
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Title | Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / CRISPR-Cas9 / Nme1Cas9 / NmeCas9 / anti-CRISPR / AcrIIC2 / HYDROLASE-HYDROLASE INHIBITOR 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Cheng, Z. / Huang, X. / Sun, W. / Wang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2. Authors: Thavalingam, A. / Cheng, Z. / Garcia, B. / Huang, X. / Shah, M. / Sun, W. / Wang, M. / Harrington, L. / Hwang, S. / Hidalgo-Reyes, Y. / Sontheimer, E.J. / Doudna, J. / Davidson, A.R. / ...Authors: Thavalingam, A. / Cheng, Z. / Garcia, B. / Huang, X. / Shah, M. / Sun, W. / Wang, M. / Harrington, L. / Hwang, S. / Hidalgo-Reyes, Y. / Sontheimer, E.J. / Doudna, J. / Davidson, A.R. / Moraes, T.F. / Wang, Y. / Maxwell, K.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jdj.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jdj.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jdj_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 6jdj_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 6jdj_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6jdj_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/6jdj ftp://data.pdbj.org/pub/pdb/validation_reports/jd/6jdj | HTTPS FTP |
-Related structure data
Related structure data | 6jd7SC 6jdxC 6n05C 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: 14196.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Gene: CIJ84_02100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E2QCQ3 #2: Protein | | Mass: 8791.206 Da / Num. of mol.: 1 / Fragment: partial Nme1Cas9 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 #3: 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: 3.5 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 7 / Details: 0.1M HEPES 7.9, 14% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 16424 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.045 / Rrim(I) all: 0.161 / Χ2: 0.947 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 803 / CC1/2: 0.815 / Rpim(I) all: 0.301 / Rrim(I) all: 0.952 / Χ2: 0.902 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JD7 Resolution: 2.6→38.673 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.673 Å
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Refine LS restraints |
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LS refinement shell |
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