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Yorodumi- PDB-8f3k: Anti-CRISPR protein AcrIIC5 inhibits CRISPR-Cas9 by acting as a D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f3k | |||||||||
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Title | Anti-CRISPR protein AcrIIC5 inhibits CRISPR-Cas9 by acting as a DNA mimic | |||||||||
Components | ACRIIC5Nch | |||||||||
Keywords | PROTEIN BINDING / Anti-CRISPR / CRISPR-Cas / Cas9 / inhibition | |||||||||
Function / homology | AMMONIUM ION / Uncharacterized protein Function and homology information | |||||||||
Biological species | Neisseria chenwenguii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | |||||||||
Authors | Shah, M. / Sungwon, H. / Davidson, A.R. / Maxwell, K.L. / Moraes, T.F. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2023 Title: Anti-CRISPR Protein AcrIIC5 Inhibits CRISPR-Cas9 by Occupying the Target DNA Binding Pocket. Authors: Hwang, S. / Shah, M. / Garcia, B. / Hashem, N. / Davidson, A.R. / Moraes, T.F. / 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 | 8f3k.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f3k.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 8f3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f3k_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 8f3k_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 8f3k_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 8f3k_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/8f3k ftp://data.pdbj.org/pub/pdb/validation_reports/f3/8f3k | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14554.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The dataset used is selenium labelled hence Met 87 is labelled as MSE Source: (gene. exp.) Neisseria chenwenguii (bacteria) / Gene: BG910_04735 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A220S190 | ||||||
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#2: Chemical | ChemComp-TRS / | ||||||
#3: Chemical | ChemComp-NH4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5 and 2.0M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.5 Å / Num. obs: 14852 / % possible obs: 96.77 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.1→38.5 Å / Rmerge(I) obs: 0.0817 / Num. unique obs: 8432 / % possible all: 96.77 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→38.5 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.5 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: -6.5386 Å / Origin y: 13.1397 Å / Origin z: -9.1798 Å
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Refinement TLS group | Selection details: (chain A and resid 11:124) |