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- PDB-1ddl: DESMODIUM YELLOW MOTTLE TYMOVIRUS -

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Basic information

Entry
Database: PDB / ID: 1ddl
TitleDESMODIUM YELLOW MOTTLE TYMOVIRUS
Components
  • DESMODIUM YELLOW MOTTLE VIRUS
  • RNA (5'-R(P*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVirus/RNA / PLANT VIRUS / DYMV / CAPSID PROTEIN / COAT PROTEIN / TYMOVIRUSES / WATER STRUCTURE / RNA / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


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
RNA / Virion protein
Similarity search - Component
Biological speciesDesmodium yellow mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLarson, S.B. / Day, J. / Canady, M.A. / Greenwood, A. / McPherson, A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Refined structure of desmodium yellow mottle tymovirus at 2.7 A resolution.
Authors: Larson, S.B. / Day, J. / Canady, M.A. / Greenwood, A. / McPherson, A.
History
DepositionNov 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
E: RNA (5'-R(P*UP*U)-3')
A: DESMODIUM YELLOW MOTTLE VIRUS
B: DESMODIUM YELLOW MOTTLE VIRUS
C: DESMODIUM YELLOW MOTTLE VIRUS


Theoretical massNumber of molelcules
Total (without water)62,7015
Polymers62,7015
Non-polymers00
Water5,134285
1
D: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
E: RNA (5'-R(P*UP*U)-3')
A: DESMODIUM YELLOW MOTTLE VIRUS
B: DESMODIUM YELLOW MOTTLE VIRUS
C: DESMODIUM YELLOW MOTTLE VIRUS
x 60


Theoretical massNumber of molelcules
Total (without water)3,762,047300
Polymers3,762,047300
Non-polymers00
Water4,324240
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
D: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
E: RNA (5'-R(P*UP*U)-3')
A: DESMODIUM YELLOW MOTTLE VIRUS
B: DESMODIUM YELLOW MOTTLE VIRUS
C: DESMODIUM YELLOW MOTTLE VIRUS
x 5


  • icosahedral pentamer
  • 314 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)313,50425
Polymers313,50425
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
D: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
E: RNA (5'-R(P*UP*U)-3')
A: DESMODIUM YELLOW MOTTLE VIRUS
B: DESMODIUM YELLOW MOTTLE VIRUS
C: DESMODIUM YELLOW MOTTLE VIRUS
x 6


  • icosahedral 23 hexamer
  • 376 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)376,20530
Polymers376,20530
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
E: RNA (5'-R(P*UP*U)-3')
A: DESMODIUM YELLOW MOTTLE VIRUS
B: DESMODIUM YELLOW MOTTLE VIRUS
C: DESMODIUM YELLOW MOTTLE VIRUS
x 5


  • crystal asymmetric unit, crystal frame
  • 314 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)313,50425
Polymers313,50425
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)348.546, 348.546, 348.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Cell settingtetragonal
Space group name H-MP4232
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Components on special symmetry positions
IDModelComponents
11C-2006-

HOH

21C-2702-

HOH

31C-2703-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)

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Components

#1: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2098.203 Da / Num. of mol.: 1 / Fragment: VIRAL RNA FRAGMENT / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(P*UP*U)-3')


Mass: 567.374 Da / Num. of mol.: 1 / Fragment: VIRAL RNA FRAGMENT / Source method: obtained synthetically
#3: Protein DESMODIUM YELLOW MOTTLE VIRUS


Mass: 20011.734 Da / Num. of mol.: 3 / Fragment: VIRAL COAT PROTEIN / Source method: isolated from a natural source / Source: (natural) Desmodium yellow mottle virus / Genus: Tymovirus / References: UniProt: O89511
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 11

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, both sitting drop, hanging drop / pH: 4.8
Details: 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM FORMATE11
2SODIUM ACETATE11
3POTASSIUM PHOSPHATE BUFFER11
4SODIUM FORMATE12
5SODIUM ACETATE12
6POTASSIUM PHOSPHATE BUFFER12
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
22.0-2.2 Msodium formate1reservoir
30.1 Msodium acetate1reservoir
41
51
61

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 178705 / Num. obs: 178705 / % possible obs: 68.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.453 / % possible all: 82.7
Reflection
*PLUS
% possible obs: 91.3 % / Num. measured all: 574527

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TURNIP YELLOW MOSAIC VIRUS

Resolution: 2.7→40 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): 3 / σ(I): 1.5
Stereochemistry target values: ENGH & HUBER FOR PROTEIN, X-PLOR PARAMETER FILE FOR RNA: DNA-RNA-ALLH3NEW.PARAM
Details: SIMULATED ANNEALING AND CONJUGATE GRADIENT MINIMIZATION
RfactorNum. reflection% reflectionSelection details
Rfree0.159 13357 9.9 %RANDOM
Rwork0.151 ---
all0.206 178705 --
obs0.152 134454 68.7 %-
Displacement parametersBiso mean: 33.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 182 0 285 4670
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na0.015
X-RAY DIFFRACTIONx_bond_d_prot0.01
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_na2.38
X-RAY DIFFRACTIONx_angle_deg_prot1.9
X-RAY DIFFRACTIONx_dihedral_angle_d20.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na39.3
X-RAY DIFFRACTIONx_dihedral_angle_d_prot20.3
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na2.93
X-RAY DIFFRACTIONx_improper_angle_d_prot1.32
X-RAY DIFFRACTIONx_mcbond_it3.611.5
X-RAY DIFFRACTIONx_mcangle_it5.862
X-RAY DIFFRACTIONx_scbond_it13.712
X-RAY DIFFRACTIONx_scangle_it23.412.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.241 716 9.5 %
Rwork0.221 6860 -
obs--39.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parhcsdx.protophcsdx.pro
X-RAY DIFFRACTION2dna-rna-allh3new.paramdna-rna.top
X-RAY DIFFRACTION3param19.sol
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 40 Å / σ(F): 3 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.241 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.221

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