+Open data
-Basic information
Entry | Database: PDB / ID: 5wtk | ||||||
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Title | Crystal structure of RNP complex | ||||||
Components |
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Keywords | HYDROLASE/RNA / HYDROLASE-RNA complex | ||||||
Function / homology | defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a Function and homology information | ||||||
Biological species | Leptotrichia shahii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å | ||||||
Authors | Liu, L. / Wang, Y. | ||||||
Citation | Journal: Cell / Year: 2017 Title: Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities Authors: Liu, L. / Li, X. / Wang, J. / Wang, M. / Chen, P. / Yin, M. / Li, J. / Sheng, G. / Wang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wtk.cif.gz | 284.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wtk.ent.gz | 220 KB | Display | PDB format |
PDBx/mmJSON format | 5wtk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/5wtk ftp://data.pdbj.org/pub/pdb/validation_reports/wt/5wtk | HTTPS FTP |
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-Related structure data
Related structure data | 5wtjSC 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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-Components
#1: Protein | Mass: 167624.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptotrichia shahii (strain DSM 19757 / CCUG 47503 / CIP 107916 / JCM 16776 / LB37) (bacteria) Strain: DSM 19757 / CCUG 47503 / CIP 107916 / JCM 16776 / LB37 Gene: c2c2 / Production host: Escherichia coli (E. coli) References: UniProt: P0DOC6, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 18533.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leptotrichia shahii (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: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium malonate, 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 53055 / % possible obs: 98.5 % / Redundancy: 4.6 % / Net I/σ(I): 13.4 |
Reflection shell | Rmerge(I) obs: 0.625 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WTJ Resolution: 2.651→40.405 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 33.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.651→40.405 Å
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Refine LS restraints |
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LS refinement shell |
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