+Open data
-Basic information
Entry | Database: PDB / ID: 5vw1 | |||||||||
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Title | Crystal structure of SpyCas9-sgRNA-AcrIIA4 ternary complex | |||||||||
Components |
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Keywords | HYDROLASE / Type II CRISPR-Cas endonculease: Cas9: Structure: Endonuclease: anti-CRISPR protein: Inhibition of Cas9: RuvC catalytic pocket: Sequence-specific PAM recognition: Genome editing tool | |||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Streptococcus pyogenes serotype M1 (bacteria) Listeria monocytogenes serotype 4a Listeria monocytogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å | |||||||||
Authors | Yang, H. / Patel, D.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mol. Cell / Year: 2017 Title: Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9. Authors: Yang, H. / Patel, D.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vw1.cif.gz | 687.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vw1.ent.gz | 557.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vw1_validation.pdf.gz | 504.6 KB | Display | wwPDB validaton report |
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Full document | 5vw1_full_validation.pdf.gz | 528.3 KB | Display | |
Data in XML | 5vw1_validation.xml.gz | 54.8 KB | Display | |
Data in CIF | 5vw1_validation.cif.gz | 77 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/5vw1 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/5vw1 | HTTPS FTP |
-Related structure data
Related structure data | 4zt0S S: Starting model for refinement |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 158732.891 Da / Num. of mol.: 1 / Mutation: D10A/H840A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Gene: cas9, csn1, SPy_1046 / Plasmid: pRSFDuet-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
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#3: Protein | Mass: 10326.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serotype 4a (strain M7) (bacteria) Strain: M7 / Gene: LMM7_0114 / Plasmid: pRSF-Duet-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E0UT28 |
-RNA chain , 1 types, 1 molecules C
#2: RNA chain | Mass: 27400.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: sgRNA was prepared by in vitro transcription / Source: (synth.) Listeria monocytogenes (bacteria) |
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-Non-polymers , 5 types, 196 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | hypothetical protein LMOG_02993 [Listeria monocytogenes J0161] GenBank: AEO04689.1 |
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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: 2.84 Å3/Da / Density % sol: 56.66 % / Mosaicity: 0.305 ° |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.2 / Details: 0.1 M HEPES (pH 7.5), and 15% PEG3350 (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2016 / Details: LR-Design detector positioner | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.598→50 Å / Num. obs: 65656 / % possible obs: 94.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 48.71 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.048 / Rrim(I) all: 0.104 / Χ2: 0.875 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZT0 Resolution: 2.598→48.021 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.17 / 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: 2.598→48.021 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -22.2824 Å / Origin y: -27.0876 Å / Origin z: 42.5557 Å
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Refinement TLS group | Selection details: all |