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Yorodumi- PDB-2i8e: Structure of SSO1404, a predicted DNA repair-associated protein f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i8e | ||||||
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Title | Structure of SSO1404, a predicted DNA repair-associated protein from Sulfolobus solfataricus P2 | ||||||
Components | Hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / DNA REPAIR / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PSI / Protein Structure Initiative | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å | ||||||
Authors | Wang, S. / Zimmerman, M.D. / Kudritska, M. / Chruszcz, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. Authors: Beloglazova, N. / Brown, G. / Zimmerman, M.D. / Proudfoot, M. / Makarova, K.S. / Kudritska, M. / Kochinyan, S. / Wang, S. / Chruszcz, M. / Minor, W. / Koonin, E.V. / Edwards, A.M. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE, HOWEVER, THAT THIS BIOLOGICAL ASSEMBLY HAS NOT BEEN EXPERIMENTALLY GENERATED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i8e.cif.gz | 31.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i8e.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 2i8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i8e_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 2i8e_full_validation.pdf.gz | 420.8 KB | Display | |
Data in XML | 2i8e_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 2i8e_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/2i8e ftp://data.pdbj.org/pub/pdb/validation_reports/i8/2i8e | HTTPS FTP |
-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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Components on special symmetry positions |
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Details | The biological assembly has not been determined experimentally. The biological unit is predicted by the PITA server (http://http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pita/RunPita.pl) to be a dimer. The second part of the predicted biological assembly is generated by the operation: -x, -y-1, z. |
-Components
#1: Protein | Mass: 12093.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: SSO1404 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: Q97YC2 | ||
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#2: Chemical | ChemComp-IOD / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystallized in 0.2M Na iodide, 20% PEG3350, 2% isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 9, 2006 / Details: Mirrors |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. all: 12619 / Num. obs: 12619 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 63.9 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 8.2 / Num. unique all: 1219 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.59→24.94 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.102 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / 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: 20.862 Å2
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Refine analyze | Luzzati coordinate error obs: 0.205 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→24.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.633 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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