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- PDB-1e57: PHYSALIS MOTTLE VIRUS: EMPTY CAPSID -

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Basic information

Entry
Database: PDB / ID: 1.0E+57
TitlePHYSALIS MOTTLE VIRUS: EMPTY CAPSID
ComponentsPHYSALIS MOTTLE VIRUS
KeywordsVIRUS / COAT PROTEIN (VIRAL) / 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 speciesPHYSALIS MOTTLE VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKrishna, S.S. / Sastri, M. / Savithri, H.S. / Murthy, M.R.N.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Structural Studies on the Empty Capsids of Physalis Mottle Virus
Authors: Krishna, S.S. / Sastri, M. / Savithri, H.S. / Murthy, M.R.N.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Three Dimensional Structure of Physalis Movirus: Implications for the Viral Assembly
Authors: Krishna, S.S. / Hiremath, C.N. / Munshi, S.K. / Prahadeeswaran, D. / Sastri, M. / Savithri, H.S. / Murthy, M.R.N.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Identification of a Discrete Intermediate in the Assembly/Disassembly of Physalis Mottle Tymovirus Through Mutational Analysis
Authors: Sastri, M. / Reddy, S. / Krishna, S.S. / Murthy, M.R.N. / Savithri, H.S.
#3: Journal: J.Mol.Biol. / Year: 1997
Title: Assembly of Physalis Mottle Virus Capsid Protein in Escherichia Coli and the Role of Amino and Carboxy Termini in the Formation of the Icosahedral Particles
Authors: Sastri, M. / Kekuda, R. / Gopinath, K. / Kumar, C.T.R. / Jagath, J.R. / Savithri, H.S.
#4: Journal: Virology / Year: 1993
Title: Architecture of Physalis Mottle Tymovirus as Probed by Monoclonal Antibodies and Cross-Linking Studies
Authors: Kekuda, R. / Karande, A.A. / Jacob, A.N.K. / Savithri, H.S.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Structure of Belladonna Mottle Virus: Cross-Rotation Function Studies with Southern Bean Mosaic Virus
Authors: Hiremath, C.N. / Munshi, S.K. / Murthy, M.R.N.
#6: Journal: J.Biol.Chem. / Year: 1989
Title: Primary Structure of Belladonna Mottle Virus Coat Protein
Authors: Suryanarayana, S. / Rao, N.A. / Murthy, M.R.N. / Savithri, H.S.
#7: Journal: J.Gen.Virol. / Year: 1987
Title: Stability of Belladonna Mottle Virus Particles: The Role of Polyamines and Calcium
Authors: Savithri, H.S. / Munshi, S.K. / Suryanarayana, S. / Divakar, S. / Murthy, M.R.N.
#8: Journal: Acta Crystallogr.,Sect.B / Year: 1987
Title: Symmetry of Belladonna Mottle Virus: Rotation Function Studies
Authors: Munshi, S.K. / Hiremath, C.N. / Murthy, M.R.N. / Savithri, H.S.
History
DepositionJul 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHYSALIS MOTTLE VIRUS
B: PHYSALIS MOTTLE VIRUS
C: PHYSALIS MOTTLE VIRUS


Theoretical massNumber of molelcules
Total (without water)59,9703
Polymers59,9703
Non-polymers00
Water00
1
A: PHYSALIS MOTTLE VIRUS
B: PHYSALIS MOTTLE VIRUS
C: PHYSALIS MOTTLE VIRUS
x 60


Theoretical massNumber of molelcules
Total (without water)3,598,186180
Polymers3,598,186180
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: PHYSALIS MOTTLE VIRUS
B: PHYSALIS MOTTLE VIRUS
C: PHYSALIS MOTTLE VIRUS
x 5


  • icosahedral pentamer
  • 300 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)299,84915
Polymers299,84915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: PHYSALIS MOTTLE VIRUS
B: PHYSALIS MOTTLE VIRUS
C: PHYSALIS MOTTLE VIRUS
x 6


  • icosahedral 23 hexamer
  • 360 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)359,81918
Polymers359,81918
Non-polymers00
Water0
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
A: PHYSALIS MOTTLE VIRUS
B: PHYSALIS MOTTLE VIRUS
C: PHYSALIS MOTTLE VIRUS
x 60


  • crystal asymmetric unit, crystal frame
  • 3.6 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)3,598,186180
Polymers3,598,186180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
identity operation1_555x,y,z1
point symmetry operation59
Unit cell
Length a, b, c (Å)289.640, 287.722, 295.226
Angle α, β, γ (deg.)63.59, 61.39, 62.94
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein PHYSALIS MOTTLE VIRUS


Mass: 19989.924 Da / Num. of mol.: 3 / Fragment: EMPTY CAPSID
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSALIS MOTTLE VIRUS / Plasmid: PET3D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36351

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growpH: 5.6
Details: PH 5.6 SODIUM ACETATE; WITH 20% PEG AS PRECIPITANT.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
180-100 mg/mlprotein11
20.5 Msodium acetate11
310 mMdithiothreitol11
42 mM11CaCl2
52-4 %(w/v)PEG800011

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 605968 / % possible obs: 36 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.149

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Processing

Software
NameVersionClassification
CNS0.4refinement
XDSdata reduction
MARSCALEdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJZ

1qjz


Resolution: 3.2→10 Å / Data cutoff high absF: 10000000 / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.296 --
Rwork0.279 --
obs0.279 263841 22.6 %
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 0 0 3742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: STRICT
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.35

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