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Yorodumi- PDB-5w1i: Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (20-n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w1i | ||||||
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Title | Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (20-nt spacer) | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Nuclease RNA binding protein / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | IODIDE ION / RNA / RNA (> 10) / LbaCas13a (C2c2) Function and homology information | ||||||
Biological species | Lachnospiraceae bacterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Knott, G.J. / Doudna, J.A. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Authors: Knott, G.J. / East-Seletsky, A. / Cofsky, J.C. / Holton, J.M. / Charles, E. / O'Connell, M.R. / Doudna, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w1i.cif.gz | 615.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w1i.ent.gz | 489 KB | Display | PDB format |
PDBx/mmJSON format | 5w1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w1i_validation.pdf.gz | 479 KB | Display | wwPDB validaton report |
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Full document | 5w1i_full_validation.pdf.gz | 499.7 KB | Display | |
Data in XML | 5w1i_validation.xml.gz | 97.5 KB | Display | |
Data in CIF | 5w1i_validation.cif.gz | 142.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/5w1i ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w1i | HTTPS FTP |
-Related structure data
Related structure data | 5w1hSC 5wlhC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: RNA chain | Mass: 16889.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Lachnospiraceae bacterium (bacteria) #2: Protein | Mass: 169192.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lachnospiraceae bacterium (bacteria) / Gene: NK4A179 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): 2DE3 / References: UniProt: A0A2D0TCG9*PLUS #3: Chemical | ChemComp-IOD / #4: 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: 2.26 Å3/Da / Density % sol: 45.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium iodide, 20 - 25 % PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.57 Å / Num. obs: 161267 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.466 / % possible all: 96.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W1H Resolution: 2.2→48.42 Å / SU ML: 0.295 / Cross valid method: FREE R-VALUE / σ(F): 1.959 / Phase error: 25.872
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.42 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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