+Open data
-Basic information
Entry | Database: PDB / ID: 5xbl | ||||||
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Title | Structure of nuclease in complex with associated protein | ||||||
Components |
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Keywords | HYDROLASE/RNA / nuclease / HYDROLASE-RNA complex | ||||||
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 (bacteria) Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.052 Å | ||||||
Authors | Dong, D. / Guo, M. / Wang, S. / Zhu, Y. / Huang, Z. | ||||||
Citation | Journal: Nature / Year: 2017 Title: Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein Authors: Guo, M. / Wang, S. / Zhu, Y. / Wang, S. / Xiong, Z. / Yang, J. / Xu, Z. / Huang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xbl.cif.gz | 338.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xbl.ent.gz | 263.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xbl_validation.pdf.gz | 468.2 KB | Display | wwPDB validaton report |
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Full document | 5xbl_full_validation.pdf.gz | 494 KB | Display | |
Data in XML | 5xbl_validation.xml.gz | 51.3 KB | Display | |
Data in CIF | 5xbl_validation.cif.gz | 70 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/5xbl ftp://data.pdbj.org/pub/pdb/validation_reports/xb/5xbl | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 158699.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Gene: cas9, csn1, SPy_1046 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
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#2: Protein | Mass: 10182.073 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A247D711*PLUS |
#3: RNA chain | Mass: 31689.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
-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: 48.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl, pH 6.5, 0.2 M MgCl2 and 14% (w/v) Polyethylene glycol (PEG) 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 45371 / % possible obs: 96.8 % / Redundancy: 3.2 % / Net I/σ(I): 10.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.052→41.78 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.052→41.78 Å
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Refine LS restraints |
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LS refinement shell |
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