+Open data
-Basic information
Entry | Database: PDB / ID: 2x4j | ||||||
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Title | Crystal structure of ORF137 from Pyrobaculum spherical virus | ||||||
Components | HYPOTHETICAL PROTEIN ORF137 | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | SH3 type barrels. - #600 / Domain of unknown function DUF5608 / Domain of unknown function DUF5607 / Domain of unknown function (DUF5607) / Domain of unknown function (DUF5608) / SH3 type barrels. / Roll / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | PYROBACULUM SPHERICAL VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å | ||||||
Authors | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
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 | 2x4j.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x4j.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 2x4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x4j_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 2x4j_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 2x4j_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 2x4j_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4j ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4j | 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 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C 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: 14967.177 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROBACULUM SPHERICAL VIRUS / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6ZYJ4 |
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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: 1.89 Å3/Da / Density % sol: 34.9 % / Description: NONE |
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Crystal grow | pH: 7 Details: 23% PEG3350, 0.37M MA-SCN, 0.23M MGCL2, 0.1M MES, PH 7.0. CRYSTAL CRYOPROTECTED WITH 40% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2008 / 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: 1.62→44.9 Å / Num. obs: 22381 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.62→1.74 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.7 / % possible all: 90.1 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.62→44.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.902 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.091 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.001 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→44.9 Å
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Refine LS restraints |
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