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- PDB-5u33: Crystal structure of AacC2c1-sgRNA-extended non-target DNA ternar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u33 | |||||||||
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Title | Crystal structure of AacC2c1-sgRNA-extended non-target DNA ternary complex | |||||||||
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![]() | HYDROLASE/DNA / 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-DNA complex | |||||||||
Function / homology | ![]() endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yang, H. / Gao, P. / Rajashankar, K.R. / Patel, D.J. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 622.3 KB | Display | ![]() |
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PDB format | ![]() | 507.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5u30C ![]() 5u31SC ![]() 5u34C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 130762.211 Da / Num. of mol.: 1 / Fragment: CRISPR-associated endonuclease AacC2c1 / Mutation: D570A/E848A/D977A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B Gene: c2c1, N007_06525 / Plasmid: pRSFDuet-SUMO / Production host: ![]() ![]() 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.) ![]() |
#3: DNA chain | Mass: 8532.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: DNA chain | Mass: 8532.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#5: Chemical | ChemComp-SO4 / |
Compound details | the position of TTTT could not be definitely determined within the poly-T sequence of the non- ...the position of TTTT could not be definitely determined within the poly-T sequence of the non-target DNA strand. The poly T fragment is thus arbitrary numbered 101-118. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.86 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.2 Details: 0.2 M ammonium acetate, 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2016 / Details: DECTRIS PILATUS 6M-F |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.75→50 Å / Num. obs: 21992 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 134.01 Å2 / CC1/2: 0.995 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.75→4.05 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.6 / CC1/2: 0.399 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5U31 Resolution: 3.75→47.492 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.26 / 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: 3.75→47.492 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: -27.1941 Å / Origin y: -24.6263 Å / Origin z: -40.1752 Å
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Refinement TLS group | Selection details: all |