+Open data
-Basic information
Entry | Database: PDB / ID: 3i4h | ||||||
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Title | Crystal structure of Cas6 in Pyrococcus furiosus | ||||||
Components | endoribonuclease | ||||||
Keywords | HYDROLASE / endoribonuclease | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Carte, J. / Wang, R. / Li, H. / Terns, R.M. / Terns, M.P. | ||||||
Citation | Journal: Genes Dev. / Year: 2008 Title: Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes Authors: Carte, J. / Wang, R. / Li, H. / Terns, R.M. / Terns, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i4h.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i4h.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 3i4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i4h_validation.pdf.gz | 424.7 KB | Display | wwPDB validaton report |
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Full document | 3i4h_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | 3i4h_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 3i4h_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/3i4h ftp://data.pdbj.org/pub/pdb/validation_reports/i4/3i4h | 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
#1: Protein | Mass: 31793.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1S4 |
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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: 2.66 Å3/Da / Density % sol: 53.81 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.02 M Magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 6.0, 15% v/v 2-Propanol, temperature 303K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 1.5418,1.5621,1.7321 | ||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2008 / Details: mirror | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→20.5 Å / Num. all: 29842 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 17.7 % / Rsym value: 0.059 / Net I/σ(I): 2.4 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 17.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.059 / % possible all: 48 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→20.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.294 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.312 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.305 Å / Total num. of bins used: 20
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