+Open data
-Basic information
Entry | Database: PDB / ID: 4txd | ||||||
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Title | Crystal structure of Thermofilum pendens Csc2 | ||||||
Components | Csc2 | ||||||
Keywords | RNA BINDING PROTEIN / RRM domain / CRISPR / prokaryotic immune system / Cas7 / RNA binding / Type I-D | ||||||
Function / homology | CRISPR-associated protein Csc2 / Csc2 Crispr / metal ion binding / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermofilum pendens (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.818 Å | ||||||
Authors | Hrle, A. / Conti, E. | ||||||
Citation | Journal: Rna Biol. / Year: 2014 Title: Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family. Authors: Hrle, A. / Maier, L.K. / Sharma, K. / Ebert, J. / Basquin, C. / Urlaub, H. / Marchfelder, A. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4txd.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4txd.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 4txd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4txd_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 4txd_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 4txd_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 4txd_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/4txd ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4txd | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43402.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermofilum pendens (archaea) / Gene: Tpen_1325 / Production host: Escherichia coli (E. coli) / References: UniProt: A1RZU2 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M KCl, 0.01 M MgCl2, 5% Peg 8000 and 17% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.818→46.22 Å / Num. obs: 50368 / % possible obs: 99.77 % / Redundancy: 6.4 % / Net I/σ(I): 25.13 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1678) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 1.818→46.218 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 23.63 / 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: 1.818→46.218 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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