+Open data
-Basic information
Entry | Database: PDB / ID: 6aay | ||||||
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Title | the Cas13b binary complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Cas13b / CRISPR / crRNA / Cas / binary complex / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | RNA / RNA (> 10) / Uncharacterized protein Function and homology information | ||||||
Biological species | Bergeyella zoohelcum ATCC 43767 (bacteria) Bergeyella zoohelcum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å | ||||||
Authors | Bo, Z. / Weiwei, Y. / Yangmiao, Y. / Ouyang, S.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res. / Year: 2018 Title: Structural insights into Cas13b-guided CRISPR RNA maturation and recognition. Authors: Zhang, B. / Ye, W.W. / Ye, Y.M. / Zhou, H. / Saeed, A.F.U.H. / Chen, J. / Lin, J.Y. / Perculija, V. / Chen, Q. / Chen, C.J. / Chang, M.X. / Choudhary, M.I. / Ouyang, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aay.cif.gz | 286.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aay.ent.gz | 236.3 KB | Display | PDB format |
PDBx/mmJSON format | 6aay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aay_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 6aay_full_validation.pdf.gz | 535.7 KB | Display | |
Data in XML | 6aay_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 6aay_validation.cif.gz | 68.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/6aay ftp://data.pdbj.org/pub/pdb/validation_reports/aa/6aay | 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: 147588.750 Da / Num. of mol.: 1 / Mutation: R1177A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bergeyella zoohelcum ATCC 43767 (bacteria) Gene: HMPREF9699_02005 / Production host: Escherichia coli (E. coli) / References: UniProt: K1LVU1 |
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#2: RNA chain | Mass: 19072.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bergeyella zoohelcum (bacteria) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.15 M Sodium chloride, 0.1 M Sodium citrate (pH 5.5), 22% (w/v) Polyethylene glycol 1,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→65.58 Å / Num. obs: 47521 / % possible obs: 99.88 % / Redundancy: 20 % / Biso Wilson estimate: 50.315 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.79→2.89 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2376 / CC1/2: 0.544 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.79→65.02 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.873 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.642 Å2
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Refinement step | Cycle: 1 / Resolution: 2.79→65.02 Å
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Refine LS restraints |
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