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- PDB-6wc0: Crystal structure of AceCas9 bound with guide RNA and DNA with 5'... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wc0 | ||||||
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Title | Crystal structure of AceCas9 bound with guide RNA and DNA with 5'-NNNTC-3' PAM | ||||||
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![]() | RNA BINDING PROTEIN/RNA/DNA / DNA endonuclease / CRISPR-Cas9 / HNH / RuvC / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex | ||||||
Function / homology | ![]() endonuclease activity / defense response to virus / DNA binding / RNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Das, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The molecular basis for recognition of 5'-NNNCC-3' PAM and its methylation state by Acidothermus cellulolyticus Cas9. Authors: Das, A. / Hand, T.H. / Smith, C.L. / Wickline, E. / Zawrotny, M. / Li, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276.7 KB | Display | ![]() |
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PDB format | ![]() | 209 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.2 KB | Display | ![]() |
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Full document | ![]() | 502 KB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 54.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wbrSC S: Starting model for refinement C: citing same article ( |
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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: 109589.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 43068 / 11B / Gene: Acel_1951 / Production host: ![]() ![]() |
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#2: RNA chain | Mass: 30477.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: DNA chain | Mass: 9127.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 3060.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.57 % |
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Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, hanging drop Details: 0.04 M Citric acid, 0.06 M Bis-tris propane and 15-20% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.61→177.62 Å / Num. obs: 252772 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.058 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.61→3.95 Å / Rmerge(I) obs: 3.629 / Mean I/σ(I) obs: 1 / Num. unique obs: 63055 / CC1/2: 0.554 / Rpim(I) all: 1.003 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WBR Resolution: 3.61→94.22 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.11 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 376.41 Å2 / Biso mean: 192.494 Å2 / Biso min: 111.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.61→94.22 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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