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Yorodumi- PDB-7pq6: Crystal Structure of the Ring Nuclease 0811 mutant-S12A from Sulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pq6 | ||||||
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Title | Crystal Structure of the Ring Nuclease 0811 mutant-S12A from Sulfolobus islandicus (Sis0811) | ||||||
Components | CRISPR-associated protein, APE2256 family | ||||||
Keywords | ANTIVIRAL PROTEIN / RING NUCLEASE / CRISPR-ASSOCIATED PROTEIN / HELIX-TURN-HELIX / VIRAL RESISTANCE / CARF NUCLEOTIDE-BINDING DOMAIN / CRISPR Ring Nuclease | ||||||
Function / homology | : / SSO1393-like, winged-helix domain / CRISPR system ring nuclease SSO1393 / CRISPR system ring nuclease SSO1393-like / CRISPR-associated protein (Cas_APE2256) / CRISPR-associated protein, APE2256 family Function and homology information | ||||||
Biological species | Sulfolobus islandicus REY15A (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Molina, R. / Jensen, A.L.G. / Marchena-Hurtado, J. / Lopez-Mendez, B. / Stella, S. / Montoya, G. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Structural basis of cyclic oligoadenylate degradation by ancillary Type III CRISPR-Cas ring nucleases. Authors: Molina, R. / Jensen, A.L.G. / Marchena-Hurtado, J. / Lopez-Mendez, B. / Stella, S. / Montoya, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pq6.cif.gz | 208.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pq6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pq6_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 7pq6_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 7pq6_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 7pq6_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/7pq6 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/7pq6 | HTTPS FTP |
-Related structure data
Related structure data | 7pq2SC 7pq3C 7pqaC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 271 / Label seq-ID: 1 - 271
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 31638.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus REY15A (acidophilic) Gene: SiRe_0811 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0NH89 #2: 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: 2.39 Å3/Da / Density % sol: 48.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2M KSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→60.82 Å / Num. obs: 16673 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.945 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.67→2.714 Å / Num. unique obs: 3165 / CC1/2: 0.494 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7PQ2 Resolution: 2.67→60.82 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.808 / SU B: 33.283 / SU ML: 0.317 / Cross valid method: FREE R-VALUE / ESU R Free: 0.414 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.112 Å2
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Refinement step | Cycle: LAST / Resolution: 2.67→60.82 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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