+Open data
-Basic information
Entry | Database: PDB / ID: 2fz2 | ||||||
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Title | Structure of Turnip Yellow Mosaic Virus at 100 K | ||||||
Components |
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Keywords | Virus/RNA / Plant virus / Coat protein / Capsid protein / Tymoviruses / TYMV / RNA / Icosahedral virus / Virus-RNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Turnip yellow mosaic virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Larson, S.B. / Lucas, R.W. / McPherson, A. | ||||||
Citation | Journal: Virology / Year: 2005 Title: The RNA of turnip yellow mosaic virus exhibits icosahedral order. Authors: Larson, S.B. / Lucas, R.W. / Greenwood, A. / McPherson, A. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: Crystal structure of turnip yellow mosaic virus. Authors: Canady, M.A. / Larson, S.B. / Day, J. / McPherson, A. #2: Journal: Proteins / Year: 1995 Title: Preliminary X-ray diffraction analysis of crystals of turnip yellow mosaic virus (TYMV). Authors: Canady, M.A. / Day, J. / McPherson, A. #3: Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of an empty capsid of turnip yellow mosaic virus. Authors: van Roon, A.M. / Bink, H.H. / Plaisier, J.R. / Pleij, C.W. / Abrahams, J.P. / Pannu, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fz2.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fz2.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 2fz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/2fz2 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/2fz2 | HTTPS FTP |
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-Related structure data
Related structure data | 2fz1C 1auyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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5 |
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6 |
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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: RNA chain | Mass: 870.588 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 20207.285 Da / Num. of mol.: 3 / Fragment: Viral coat protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Turnip yellow mosaic virus / Genus: Tymovirus / Strain: (Australian isolate) / Species (production host): Brassica rapa / Production host: Brassica rapa subsp. chinensis (bok-choy) / Strain (production host): subsp. chinensis / References: UniProt: P20125 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 1.0-1.7 M NH4PO4, 0.1 M MES buffer, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.61→59.12 Å / Num. all: 247650 / Num. obs: 225845 / % possible obs: 35.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.106 / Net I/σ(I): 7.49 | ||||||||||||||||||
Reflection shell | Resolution: 2.61→2.65 Å / Redundancy: 1 % / Mean I/σ(I) obs: -0.41 / Num. unique all: 172 / % possible all: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AUY Resolution: 2.9→59.12 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 171751.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Simulated annealing and conjugate gradient minimization. Stereochemistry target values for the nucleic acid fragment are from Parkinson, Vojtechovsky, Clowney, Brunger & Berman
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3842 Å2 / ksol: 0.394524 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→59.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
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Xplor file |
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