+Open data
-Basic information
Entry | Database: PDB / ID: 1a6c | |||||||||
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Title | STRUCTURE OF TOBACCO RINGSPOT VIRUS | |||||||||
Components | TOBACCO RINGSPOT VIRUS CAPSID PROTEIN | |||||||||
Keywords | VIRUS / TRSV / NEPOVIRUS / VIRUS STRUCTURE / VIRUS EVOLUTION / PICORNAVIRUS SUPERFAMILY / VIRUS CAPSID PROTEIN / Icosahedral virus | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Tobacco ringspot virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Johnson, J.E. / Chandrasekar, V. | |||||||||
Citation | Journal: Structure / Year: 1998 Title: The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily. Authors: Chandrasekar, V. / Johnson, J.E. #1: Journal: Virology / Year: 1995 Title: Expression of Tobacco Ringspot Virus Capsid Protein and Satellite RNA in Insect Cells and Three-Dimensional Structure of Tobacco Ringspot Virus-Like Particles Authors: Singh, S. / Rothnagel, R. / Prasad, B.V. / Buckley, B. #2: Journal: Virus Res. / Year: 1995 Title: Erratum. Nucleotide Sequence and in Vitro Expression of the Capsid Protein Gene of Tobacco Ringspot Virus Authors: Buckley, B. / Silva, S. / Singh, S. #3: Journal: Virus Res. / Year: 1993 Title: Nucleotide Sequence and in Vitro Expression of the Capsid Protein Gene of Tobacco Ringspot Virus Authors: Buckley, B. / Silva, S. / Singh, S. #4: Journal: Science / Year: 1989 Title: Protein-RNA Interactions in an Icosahedral Virus at 3.0 A Resolution Authors: Chen, Z.G. / Stauffacher, C. / Li, Y. / Schmidt, T. / Bomu, W. / Kamer, G. / Shanks, M. / Lomonossoff, G. / Johnson, J.E. #5: Journal: Nature / Year: 1985 Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a6c.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6c.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6c ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6c | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 56993.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tobacco ringspot virus / Genus: Nepovirus / Strain: XANTHI-NC / References: UniProt: Q88894 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 27 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: VIRUS WAS CRYSTALLIZED USING HANGING DROP SETTING FROM RESERVOIR BUFFER CONTAINING 2-3% (W/V) PEG 3350, 1MM SODIUM AZIDE AND 0.125 M POTASSIUM PHOSPHATE, PH 6.5, pH 6.0, vapor diffusion - hanging drop |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Conc.: 2-3 % / Common name: PEG MW 3350 |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Apr 1, 1994 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 92395 / % possible obs: 18 % / Observed criterion σ(I): 4 / Redundancy: 1.2 % / Rmerge(I) obs: 0.084 / Rsym value: 0.15 |
Reflection shell | Resolution: 3.5→4 Å / % possible all: 10 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: STRUCTURE OF COMOVIRUS CPMV Resolution: 3.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 1 Details: THE STRUCTURE WAS REFINED TO 3.5 ANGSTROMS RESOLUTION USING ONLY 27% OF THE THEORETICALLY POSSIBLE UNIQUE REFLECTIONS BETWEEN 8.0 AND 3.5 ANGSTROMS. THERE ARE STILL SOME BOND ANGLES AND BOND ...Details: THE STRUCTURE WAS REFINED TO 3.5 ANGSTROMS RESOLUTION USING ONLY 27% OF THE THEORETICALLY POSSIBLE UNIQUE REFLECTIONS BETWEEN 8.0 AND 3.5 ANGSTROMS. THERE ARE STILL SOME BOND ANGLES AND BOND LENGTHS IN THE CRYSTAL STRUCTURE WHICH VARY BY GREATER THAN 3.0 RMSD FROM THEIR CORRESPONDING E & H VALUES. THESE HAVE NOT BEEN FIXED AT PRESENT.
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Displacement parameters | Biso mean: 15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.64 Å / Total num. of bins used: 8 /
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Xplor file |
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