+Open data
-Basic information
Entry | Database: PDB / ID: 5u34 | |||||||||
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Title | Crystal structure of AacC2c1-sgRNA binary complex | |||||||||
Components |
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Keywords | HYDROLASE/RNA / Type V CRISPR-Cas endonculease: C2c1: Structure: Binary complex with sgRNA: Ternary complex with added DNA: RuvC catalytic pocket: Sequence-specific PAM recognition: Genome editing tool / HYDROLASE-RNA complex | |||||||||
Function / homology | defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / RNA / RNA (> 10) / RNA (> 100) / CRISPR-associated endonuclease Cas12b Function and homology information | |||||||||
Biological species | Alicyclobacillus acidoterrestris (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.255 Å | |||||||||
Authors | Yang, H. / Gao, P. / Rajashankar, K.R. / Patel, D.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2016 Title: PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease. Authors: Yang, H. / Gao, P. / Rajashankar, K.R. / Patel, D.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u34.cif.gz | 509.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u34.ent.gz | 413.3 KB | Display | PDB format |
PDBx/mmJSON format | 5u34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/5u34 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/5u34 | HTTPS FTP |
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-Related structure data
Related structure data | 5u30C 5u31SC 5u33C C: citing same article (ref.) S: Starting model for refinement |
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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: 131835.047 Da / Num. of mol.: 1 / Fragment: CRISPR-associated endonuclease AacC2c1 / Mutation: E848A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidoterrestris (bacteria) Strain: ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B Gene: c2c1, N007_06525 / Plasmid: pRSFDuet-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: T0D7A2, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 36183.555 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Alicyclobacillus acidoterrestris (bacteria) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.41 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.2 Details: 0.2 M lithium sulfate, 0.1 M HEPES (pH 7.5), and 25% PEG3350 (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2016 / Details: LR-Design detector positioner |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. obs: 26140 / % possible obs: 99.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 106.74 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.25→3.48 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1 / CC1/2: 0.318 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U31 Resolution: 3.255→48.33 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.19 / 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: 3.255→48.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.8668 Å / Origin y: -23.3861 Å / Origin z: -26.9779 Å
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Refinement TLS group | Selection details: all |