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Yorodumi- PDB-2x5t: Crystal structure of ORF131 from Sulfolobus islandicus rudivirus 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x5t | ||||||
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Title | Crystal structure of ORF131 from Sulfolobus islandicus rudivirus 1 | ||||||
Components | ORF 131 | ||||||
Keywords | VIRAL PROTEIN / DOMAIN-SWAP / ARCHEAL VIRUS | ||||||
Function / homology | Signal recognition particle alu RNA binding heterodimer, srp9/1 - #60 / : / PHA01746-like protein / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta / MALONATE ION / Uncharacterized protein 131 Function and homology information | ||||||
Biological species | SULFOLOBUS ISLANDICUS RUDIVIRUS 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Naismith, J.H. / White, M.F. | ||||||
Citation | Journal: J.Struct.Funct.Genomics / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x5t.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x5t.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 2x5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x5t_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
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Full document | 2x5t_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 2x5t_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 2x5t_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/2x5t ftp://data.pdbj.org/pub/pdb/validation_reports/x5/2x5t | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gSC 2x5hC 2x5pC 2x5qC 2x5rC 2x7bC 2x7iC 2xu2C C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11031.764 Da / Num. of mol.: 1 / Fragment: TRUNCATED VERSION, RESIDUES 2-96 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS ISLANDICUS RUDIVIRUS 1 / Variant: XX / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BL21 / References: UniProt: Q8QL44 |
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#2: Chemical | ChemComp-MLI / |
#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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | Details: 2.1 M SODIUM MALONATE AND CRYOPROTECTED WITH 2.4 M MALONATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 6828 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 12 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X5G Resolution: 2.2→50.06 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.682 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.914 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50.06 Å
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Refine LS restraints |
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