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- PDB-1opo: THE STRUCTURE OF CARNATION MOTTLE VIRUS -

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Basic information

Entry
Database: PDB / ID: 1opo
TitleTHE STRUCTURE OF CARNATION MOTTLE VIRUS
ComponentsCoat protein
KeywordsVIRUS / PLANT VIRUS / CARMOVIRUS / VIRUS/VIRAL PROTEIN / TOMATO BUSHY STUNT VIRUS / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / RNA binding
Similarity search - Function
Carmovirus coat protein / Coat protein, C-terminal, Carmoviral / Carmovirus coat protein / Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Immunoglobulin-like ...Carmovirus coat protein / Coat protein, C-terminal, Carmoviral / Carmovirus coat protein / Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCarnation mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMorgunova, E. / Dauter, Z. / Fry, E. / Stuart, D. / Stel'mashchuk, V. / Mikhailov, A.M. / Wilson, K.S. / Vainshtein, B.K.
CitationJournal: Febs Lett. / Year: 1994
Title: The atomic structure of Carnation Mottle Virus capsid protein
Authors: Morgunova, E. / Dauter, Z. / Fry, E. / Stuart, D. / Stel'mashchuk, V. / Mikhailov, A.M. / Wilson, K.S. / Vainshtein, B.K.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8197
Polymers113,4913
Non-polymers3284
Water00
1
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,829,135420
Polymers6,809,439180
Non-polymers19,696240
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: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 5


  • icosahedral pentamer
  • 569 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)569,09535
Polymers567,45315
Non-polymers1,64120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 683 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)682,91442
Polymers680,94418
Non-polymers1,97024
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: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 569 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)569,09535
Polymers567,45315
Non-polymers1,64120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)382.6, 382.6, 382.6
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)
3generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5)
4generate(-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5)
5generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)

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Components

#1: Protein Coat protein


Mass: 37830.219 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Carnation mottle virus / Genus: Carmovirus / References: UniProt: P04383
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.03
Details: 0.1M Tris-maleic (mal)/NaOH, 25% saturated ammonium sulphate, 1.7-heptandiol or PEG 300 were added to lessen the number of pellets, pH 5.03, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris-HCl1drop
240-50 mg/mlvirus1drop
310 %satammonium sulfate1drop
40.1 MTris-maleic/NaOH1reservoirpH5.03
525 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.96 Å
DetectorType: HENDRIX-LENTFER / Detector: IMAGE PLATE / Date: Jul 15, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 3.2→6 Å / Num. all: 140483 / Num. obs: 140483 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.082
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 6 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
GAP(Oxford)model building
X-PLOR2.1refinement
GAP(OXFORD)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TBV

2tbv


Resolution: 3.2→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / StereochEM target val spec case: RANDOM / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
all0.183 140248 -
obs0.183 140248 -
Rfree--Random
Refinement stepCycle: LAST / Resolution: 3.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 16 0 6130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_angle_deg4.15
Refinement
*PLUS
Highest resolution: 3.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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