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- PDB-6jdx: Crystal structure of AcrIIC2 dimer in complex with partial Nme1Ca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jdx | ||||||
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Title | Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9 preprocessed with protease alpha-Chymotrypsin | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / CRISPR-Cas9 / Nme1Cas9 / NmeCas9 / anti-CRISPR / AcrIIC2 / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, Z. / Huang, X. / Sun, W. / Wang, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2. Authors: Thavalingam, A. / Cheng, Z. / Garcia, B. / Huang, X. / Shah, M. / Sun, W. / Wang, M. / Harrington, L. / Hwang, S. / Hidalgo-Reyes, Y. / Sontheimer, E.J. / Doudna, J. / Davidson, A.R. / ...Authors: Thavalingam, A. / Cheng, Z. / Garcia, B. / Huang, X. / Shah, M. / Sun, W. / Wang, M. / Harrington, L. / Hwang, S. / Hidalgo-Reyes, Y. / Sontheimer, E.J. / Doudna, J. / Davidson, A.R. / Moraes, T.F. / Wang, Y. / Maxwell, K.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.8 KB | Display | ![]() |
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PDB format | ![]() | 51.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.5 KB | Display | ![]() |
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Full document | ![]() | 460.4 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jd7SC ![]() 6jdjC ![]() 6n05C 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14196.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 8791.206 Da / Num. of mol.: 1 / Fragment: truncation Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: C9X1G5, Hydrolases; Acting on ester bonds #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.25 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 7.9 / Details: 0.1M HEPES pH 7.9, 14% PEG 20000 |
-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: Sep 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97894 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 21775 / % possible obs: 99.1 % / Redundancy: 10.8 % / CC1/2: 0.915 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.027 / Rrim(I) all: 0.091 / Χ2: 0.969 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 2.28→2.32 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1073 / CC1/2: 0.996 / Rpim(I) all: 0.335 / Rrim(I) all: 1.124 / Χ2: 0.937 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JD7 Resolution: 2.28→45.003 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.74
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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: 2.28→45.003 Å
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Refine LS restraints |
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LS refinement shell |
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