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Yorodumi- PDB-2fz1: Structure of Empty Head Turnip Yellow Mosaic Virus (ATC) at 100 K -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fz1 | ||||||
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Title | Structure of Empty Head Turnip Yellow Mosaic Virus (ATC) at 100 K | ||||||
Components | Coat protein | ||||||
Keywords | VIRUS / Plant virus / Coat protein / Capsid protein / Tymoviruses / TYMV / Icosahedral virus | ||||||
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 | 2fz1.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fz1.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/2fz1 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/2fz1 | HTTPS FTP |
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-Related structure data
Related structure data | 2fz2C 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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2 |
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3 |
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4 |
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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: Protein | Mass: 20207.285 Da / Num. of mol.: 3 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 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.34 Å3/Da / Density % sol: 80.6 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 1998 / Details: Vertical and toroidal focusing mirror |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→49.53 Å / Num. all: 322958 / Num. obs: 281901 / % possible obs: 63.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.35 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.118 / Net I/σ(I): 4.37 |
Reflection shell | Resolution: 2.89→2.94 Å / Redundancy: 1.15 % / Mean I/σ(I) obs: 0.41 / Num. unique all: 5433 / % possible all: 21.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AUY Resolution: 2.9→48.64 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 129062.31 / 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.1234 Å2 / ksol: 0.32222 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→48.64 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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