+Open data
-Basic information
Entry | Database: PDB / ID: 4ic1 | ||||||
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Title | Crystal structure of SSO0001 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cas4 / CRISPR / MCSG / Exonuclease / PSI-Biology / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information : / 5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming) / single-stranded DNA 5'-3' DNA exonuclease activity / DNA duplex unwinding / manganese ion binding / 4 iron, 4 sulfur cluster binding / defense response to virus / DNA binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Nocek, B. / Skarina, T. / Lemak, S. / Beloglazova, N. / Flick, R. / Brown, G. / Savchenko, A. / Joachimiak, A. / Yakunin, A.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus. Authors: Lemak, S. / Beloglazova, N. / Nocek, B. / Skarina, T. / Flick, R. / Brown, G. / Popovic, A. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ic1.cif.gz | 787 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ic1.ent.gz | 676.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ic1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/4ic1 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/4ic1 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | confirmed biologically |
-Components
#1: Protein | Mass: 23907.211 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0001 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 / References: UniProt: Q97TX9 #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SF4 / #4: 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: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% PEG 3350, 0.1M NaCitrate, 0.2M NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.35→40 Å / Num. all: 121708 / Num. obs: 118972 / % possible obs: 97.3 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.6 | ||||||||||||||||||
Reflection shell | Resolution: 2.35→2.39 Å / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.625 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 1.7 / σ(I): 2 / ESU R Free: 0.271 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.708 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.347→2.408 Å / Total num. of bins used: 20
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