[English] 日本語
Yorodumi- PDB-6k4u: Crystal structure of xCas9 in complex with sgRNA and DNA (TGA PAM) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k4u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of xCas9 in complex with sgRNA and DNA (TGA PAM) | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / endonuclease / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes serotype M1 (bacteria) Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Chen, W. / Zhang, H. / Zhang, Y. / Wang, Y. / Gan, J. / Ji, Q. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Plos Biol. / Year: 2019 Title: Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease. Authors: Chen, W. / Zhang, H. / Zhang, Y. / Wang, Y. / Gan, J. / Ji, Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6k4u.cif.gz | 662.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6k4u.ent.gz | 542.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k4u_validation.pdf.gz | 479.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6k4u_full_validation.pdf.gz | 527.3 KB | Display | |
Data in XML | 6k4u_validation.xml.gz | 52.1 KB | Display | |
Data in CIF | 6k4u_validation.cif.gz | 71.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/6k4u ftp://data.pdbj.org/pub/pdb/validation_reports/k4/6k4u | HTTPS FTP |
-Related structure data
Related structure data | 6k3zC 6k4pC 6k4qC 6k4sC 6k57C 4un3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 158538.844 Da / Num. of mol.: 1 Mutation: D10A, A262T, R324L, S409T, E480K, E543D, M694I, H840A, E1219V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Gene: cas9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
---|---|
#2: RNA chain | Mass: 26788.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
#3: DNA chain | Mass: 8567.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
#4: DNA chain | Mass: 3709.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.16 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 85 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: AGILENT EOS CCD / Detector: CCD / Date: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 36568 / % possible obs: 99 % / Redundancy: 4.8 % / CC1/2: 0.995 / Rpim(I) all: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 4.3 % / Num. unique obs: 3602 / CC1/2: 0.548 / Rpim(I) all: 0.613 / % possible all: 98.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UN3 Resolution: 3.2→49.38 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.824 / SU B: 66.918 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.657 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.627 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→49.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|