+Open data
-Basic information
Entry | Database: PDB / ID: 4uw2 | ||||||
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Title | Crystal structure of Csm1 in T.onnurineus | ||||||
Components | CSM1 | ||||||
Keywords | IMMUNE SYSTEM / BACTERIAL IMMUNITY / CRISPR / CSM INTERFERENCE CSM1 / HD DOMAIN | ||||||
Function / homology | Function and homology information exonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | THERMOCOCCUS ONNURINEUS NA1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.632 Å | ||||||
Authors | Jung, T.Y. / An, Y. / Park, K.H. / Lee, M.H. / Oh, B.H. / Woo, E.J. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Crystal Structure of the Csm1 Subunit of the Csm Complex and its Single-Stranded DNA-Specific Nuclease Activity. Authors: Jung, T. / An, Y. / Park, K. / Lee, M. / Oh, B. / Woo, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uw2.cif.gz | 374.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uw2.ent.gz | 308.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uw2_validation.pdf.gz | 479 KB | Display | wwPDB validaton report |
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Full document | 4uw2_full_validation.pdf.gz | 519.5 KB | Display | |
Data in XML | 4uw2_validation.xml.gz | 69.6 KB | Display | |
Data in CIF | 4uw2_validation.cif.gz | 96.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uw2 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uw2 | 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 89037.617 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOCOCCUS ONNURINEUS NA1 (archaea) / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 DE3 RIL / References: UniProt: B6YWB8 #2: 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: 2.6 Å3/Da / Density % sol: 52.67 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.2 M AMMONIUM CITRATE PH 7.0, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97918 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.5 |
Reflection | Resolution: 2.63→50 Å / Num. obs: 78224 / % possible obs: 98.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 40.84 |
Reflection shell | Resolution: 2.63→2.68 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 4.67 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.632→30.657 Å / σ(F): 0.19 / Phase error: 27.26 / Stereochemistry target values: TWIN_LSQ_F Details: CHAIN C AND D CONTAINS ONLY A PARTIAL DOMAIN OF FULL STRUCTURE DUE TO SPONTANEOUS PARTIAL DIGESTION DURING CRYSTALLIZATION.
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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: 2.632→30.657 Å
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Refine LS restraints |
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LS refinement shell |
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