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Yorodumi- PDB-2h36: Structure of ORF14 from Sulfolobus Islandicus Filamentous Virus (SIFV) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h36 | ||||||
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Title | Structure of ORF14 from Sulfolobus Islandicus Filamentous Virus (SIFV) | ||||||
Components | Hypothetical protein SIFV0014 | ||||||
Keywords | UNKNOWN FUNCTION / Archaea / Virus | ||||||
Function / homology | Double Stranded RNA Binding Domain - #300 / Sulfolobus islandicus filamentous virus, Orf14 / Protein of unknown function (DUF1374) / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein 14 Function and homology information | ||||||
Biological species | Sulfolobus islandicus filamentous virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å | ||||||
Authors | Goulet, A. / Spinelli, S. / Cambillau, C. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: The crystal structure of ORF14 from Sulfolobus islandicus filamentous virus Authors: Goulet, A. / Spinelli, S. / Blangy, S. / van Tilbeurgh, H. / Leulliot, N. / Basta, T. / Prangishvili, D. / Cambillau, C. / Campanacci, V. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and preliminary X-ray diffraction analysis of protein 14 from Sulfolobus islandicus filamentous virus (SIFV) Authors: Goulet, A. / Spinelli, S. / Campanacci, V. / Porciero, S. / Blangy, S. / Garrett, R.A. / van Tilbeurgh, H. / Leulliot, N. / Basta, T. / Prangishvili, D. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h36.cif.gz | 34.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h36.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 2h36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h36_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 2h36_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 2h36_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 2h36_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/2h36 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/2h36 | 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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Unit cell |
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-Components
#1: Protein | Mass: 13480.763 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus filamentous virus Genus: Betalipothrixvirus / Gene: ORF 14 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q914L6 |
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#2: 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: 3.29 Å3/Da / Density % sol: 62.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 18-26% (w/v) polyethylene glycol 4000, 0.5M MgCl2, 33mM HEPES, 0.2M imidazole malate pH 5.2-5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9798 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 4, 2006 |
Radiation | Monochromator: 2 mirrors, onemonochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→23 Å / Num. obs: 4170 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 53.4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 75 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 55 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 17 / Rsym value: 0.386 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.95→22.07 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 37.162 / SU ML: 0.331 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 4.336 / ESU R Free: 0.45 / 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: 27.377 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→22.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.952→3.027 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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