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Yorodumi- PDB-4tno: Hypothetical protein PF1117 from Pyrococcus Furiosus: Structure s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tno | ||||||
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Title | Hypothetical protein PF1117 from Pyrococcus Furiosus: Structure solved by sulfur-SAD using Swiss Light Source Data | ||||||
Components | CRISPR-associated endoribonuclease Cas2 | ||||||
Keywords | HYDROLASE / SULFUR SAD | ||||||
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 | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å | ||||||
Authors | Weinert, T. / Waltersperger, S. / Olieric, V. / Panepucci, E. / Chen, L. / Rose, J.P. / Wang, M. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: Nat.Methods / Year: 2015 Title: Fast native-SAD phasing for routine macromolecular structure determination. Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tno.cif.gz | 31.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tno.ent.gz | 19.7 KB | Display | PDB format |
PDBx/mmJSON format | 4tno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/4tno ftp://data.pdbj.org/pub/pdb/validation_reports/tn/4tno | HTTPS FTP |
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-Related structure data
Related structure data | 4pgoC 4piiC 4r8tC 4r8uC 4tn8C 4wabC 4wauC 4wbqC 4wbxC C: citing same article (ref.) |
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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
#1: Protein | Mass: 9992.677 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: cas2, PF1117 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8U1T8, Hydrolases; Acting on ester bonds | ||
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#2: Chemical | #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: 2.45 Å3/Da / Density % sol: 49.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (10 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 0.1M SODIUM CITRATE BUFFER CONTAINING 0.1 M CHES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.066 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.066 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. obs: 10426 / % possible obs: 97.1 % / Redundancy: 76.2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 71.7 |
Reflection shell | Redundancy: 3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.2 / % possible all: 65.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.14→40.948 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 0.3861 / Stereochemistry target values: MLHL
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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: 2.14→40.948 Å
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Refine LS restraints |
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LS refinement shell |
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