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Yorodumi- PDB-5wti: Crystal structure of the CRISPR-associated protein in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wti | ||||||
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Title | Crystal structure of the CRISPR-associated protein in complex with crRNA and DNA | ||||||
Components |
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Keywords | Hydrolase/DNA/RNA / CRISPR / RNA / DNA / Hydrolase-DNA-RNA complex | ||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein Function and homology information | ||||||
Biological species | Bacillus thermoamylovorans (bacteria) RNA transcription vector pBRDI1 (others) Lobariella soredians (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.682 Å | ||||||
Authors | Wu, D. / Guan, X. / Zhu, Y. / Huang, Z. | ||||||
Citation | Journal: Cell Res. / Year: 2017 Title: Structural basis of stringent PAM recognition by CRISPR-C2c1 in complex with sgRNA Authors: Wu, D. / Guan, X. / Zhu, Y. / Ren, K. / Huang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wti.cif.gz | 298.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wti.ent.gz | 237.1 KB | Display | PDB format |
PDBx/mmJSON format | 5wti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wti_validation.pdf.gz | 471.7 KB | Display | wwPDB validaton report |
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Full document | 5wti_full_validation.pdf.gz | 489 KB | Display | |
Data in XML | 5wti_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 5wti_validation.cif.gz | 58.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/5wti ftp://data.pdbj.org/pub/pdb/validation_reports/wt/5wti | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules EH
#1: DNA chain | Mass: 8782.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lobariella soredians (fungus) |
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#2: DNA chain | Mass: 3709.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lobariella soredians (fungus) |
-Protein / RNA chain , 2 types, 2 molecules ZB
#3: Protein | Mass: 130567.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thermoamylovorans (bacteria) / Gene: B4166_3744, B4167_2499 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D0F5I0 |
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#4: RNA chain | Mass: 39656.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RNA transcription vector pBRDI1 (others) Production host: RNA transcription vector pBRDI1 (others) |
-Non-polymers , 2 types, 133 molecules
#5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.08 M Strontium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate, 35% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 86779 / % possible obs: 99 % / Redundancy: 7 % / Net I/σ(I): 23.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.682→19.91 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.56 / 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: 2.682→19.91 Å
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Refine LS restraints |
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LS refinement shell |
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