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- PDB-1auy: TURNIP YELLOW MOSAIC VIRUS -

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Basic information

Entry
Database: PDB / ID: 1auy
TitleTURNIP YELLOW MOSAIC VIRUS
ComponentsTURNIP YELLOW MOSAIC VIRUS
KeywordsVIRUS / PLANT VIRUS / CAPSID PROTEIN / COAT PROTEIN / JELLYROLL / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Tymovirus coat protein / Tymovirus coat protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTurnip yellow mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT/MIR / Resolution: 3 Å
AuthorsCanady, M.A. / Larson, S.B. / Day, J. / McPherson, A.
Citation
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.
#1: 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.
History
DepositionSep 7, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TURNIP YELLOW MOSAIC VIRUS
B: TURNIP YELLOW MOSAIC VIRUS
C: TURNIP YELLOW MOSAIC VIRUS


Theoretical massNumber of molelcules
Total (without water)60,5083
Polymers60,5083
Non-polymers00
Water00
1
A: TURNIP YELLOW MOSAIC VIRUS
B: TURNIP YELLOW MOSAIC VIRUS
C: TURNIP YELLOW MOSAIC VIRUS
x 60


Theoretical massNumber of molelcules
Total (without water)3,630,471180
Polymers3,630,471180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: TURNIP YELLOW MOSAIC VIRUS
B: TURNIP YELLOW MOSAIC VIRUS
C: TURNIP YELLOW MOSAIC VIRUS
x 5


  • icosahedral pentamer
  • 303 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)302,53915
Polymers302,53915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: TURNIP YELLOW MOSAIC VIRUS
B: TURNIP YELLOW MOSAIC VIRUS
C: TURNIP YELLOW MOSAIC VIRUS
x 6


  • icosahedral 23 hexamer
  • 363 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)363,04718
Polymers363,04718
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: TURNIP YELLOW MOSAIC VIRUS
B: TURNIP YELLOW MOSAIC VIRUS
C: TURNIP YELLOW MOSAIC VIRUS
x 15


  • crystal asymmetric unit, crystal frame
  • 908 kDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)907,61845
Polymers907,61845
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)515.500, 515.500, 309.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699)128.875, -208.52413, 79.64913
3generate(-0.30901699, -0.5, -0.80901699), (0.5, -0.80901699, 0.30901699), (-0.80901699, -0.30901699, 0.5)337.39913, -128.875, 208.52413
4generate(-0.30901699, 0.5, -0.80901699), (-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5)337.39913, 128.875, 208.52413
5generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699)128.875, 208.52413, 79.64913
6generate(-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699), (-0.5, 0.80901699, 0.30901699)466.27413, 79.64913, 128.875
7generate(-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699)386.625, 208.52413, -79.64913
8generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)128.875, 208.52413, -79.64913
9generate(0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699)49.22587, 79.64913, 128.875
10generate(-1), (1), (-1)257.75, 257.75
11generate(0.80901699, -0.30901699, -0.5), (0.30901699, -0.5, 0.80901699), (-0.5, -0.80901699, -0.30901699)49.22587, -79.64913, 128.875
12generate(0.30901699, -0.5, -0.80901699), (-0.5, -0.80901699, 0.30901699), (-0.80901699, 0.30901699, -0.5)178.10087, 128.875, 208.52413
13generate(-1), (-1), (1)257.75, 257.75
14generate(0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699), (0.80901699, 0.30901699, 0.5)178.10087, 128.875, -208.52413
15generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)49.22587, -79.64913, -128.875

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Components

#1: Protein TURNIP YELLOW MOSAIC VIRUS / TYMV


Mass: 20169.281 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip yellow mosaic virus / Genus: Tymovirus / Species (production host): Brassica rapa / Production host: Brassica rapa subsp. chinensis (bok-choy) / Strain (production host): DAVIS CALIFORNIA / References: UniProt: P03608
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

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Sample preparation

CrystalDescription: CCMV WAS USED TO GENERATE INITIAL PHASES WHICH WERE THEN USED TO LOCATE HEAVY ATOM SITES.
Crystal growMethod: vapor diffusion, hanging drop / pH: 3.7
Details: 1.11 M AMMONIUM PHOSPHATE 100 MM MES PH 3.7 HANGING DROP, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.11-1.15 Mammonium phosphate1reservoir
2100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Oct 1, 1994 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 348694 / % possible obs: 73.7 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.105
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / % possible all: 4.7
Reflection
*PLUS
Rmerge(I) obs: 0.105

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT/MIR
Starting model: COWPEA CHLOROTIC MOTTLE VIRUS (CCMV)

Resolution: 3→8 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.193 23586 10.1 %RANDOM
Rwork0.187 ---
obs0.187 232638 52 %-
Displacement parametersBiso mean: 22.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.52 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 0 0 4045
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.281.5
X-RAY DIFFRACTIONx_mcangle_it6.952
X-RAY DIFFRACTIONx_scbond_it8.662
X-RAY DIFFRACTIONx_scangle_it13.132.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 361 10.3 %
Rwork0.33 3140 -
obs--4.7 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PR
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.62
LS refinement shell
*PLUS
Rfactor Rfree: 0.36 / Rfactor Rwork: 0.33

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