+Open data
-Basic information
Entry | Database: PDB / ID: 6iv9 | ||||||
---|---|---|---|---|---|---|---|
Title | the Cas13d binary complex | ||||||
Components |
| ||||||
Keywords | RNA BINDING PROTEIN/RNA / CRISPR / Cas13d / crRNA / binary complex / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | RNA / RNA (> 10) / TerB_C domain-containing protein Function and homology information | ||||||
Biological species | uncultured Ruminococcus sp (environmental samples) uncultured Ruminococcus sp. (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Zhang, B. / Ye, Y.M. / Ye, W.W. / OuYang, S.Y. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d. Authors: Zhang, B. / Ye, Y. / Ye, W. / Perculija, V. / Jiang, H. / Chen, Y. / Li, Y. / Chen, J. / Lin, J. / Wang, S. / Chen, Q. / Han, Y.S. / Ouyang, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6iv9.cif.gz | 231 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6iv9.ent.gz | 177.1 KB | Display | PDB format |
PDBx/mmJSON format | 6iv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iv9_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6iv9_full_validation.pdf.gz | 474.7 KB | Display | |
Data in XML | 6iv9_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 6iv9_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/6iv9 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/6iv9 | HTTPS FTP |
-Related structure data
Related structure data | 6iv8SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 107446.258 Da / Num. of mol.: 1 / Mutation: R288A, R823A Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured Ruminococcus sp (environmental samples) Gene: SAMEA3545300_02264 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C5SD84 | ||
---|---|---|---|
#2: RNA chain | Mass: 15899.497 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured Ruminococcus sp. (environmental samples) Production host: Escherichia coli (E. coli) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.29 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: (8% (v/v) Tacsimate (pH 7.0), 17% (w/v) Polyethylene glycol 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→100.11 Å / Num. obs: 121127 / % possible obs: 98.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 5918 / CC1/2: 0.886 / Rpim(I) all: 0.352 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IV8 Resolution: 1.86→100.11 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.369 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.102 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.41 Å2 / Biso mean: 38.134 Å2 / Biso min: 18.66 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.86→100.11 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.86→1.908 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|