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- PDB-5cw0: Investigation of RNA structure in satellite panicum mosaic virus -

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Basic information

Entry
Database: PDB / ID: 5cw0
TitleInvestigation of RNA structure in satellite panicum mosaic virus
ComponentsCoat protein
KeywordsVIRUS / capsid protein / satellite virus
Function / homologyPotexvirus coat protein / Satellite virus coat / Satellite virus coat domain superfamily / viral capsid / structural molecule activity / Coat protein
Function and homology information
Biological speciesSatellite panicum mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.6 Å
Model detailsSPMV capsid protein
AuthorsMakino, D.L. / Day, J. / Larson, S.B. / McPherson, A.
Funding support United States, Brazil, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58868-02 United States
CNPq - Conselho Nacional de Desenvolvimento Cientifico e Tecnologico Brazil
CitationJournal: Virology / Year: 2006
Title: Investigation of RNA structure in satellite panicum mosaic virus.
Authors: Makino, D.L. / Day, J. / Larson, S.B. / McPherson, A.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

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Assembly

Deposited unit
A: Coat protein


Theoretical massNumber of molelcules
Total (without water)16,9831
Polymers16,9831
Non-polymers00
Water0
1
A: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)1,018,98960
Polymers1,018,98960
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: Coat protein
x 5


  • icosahedral pentamer
  • 84.9 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)84,9165
Polymers84,9165
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
x 6


  • icosahedral 23 hexamer
  • 102 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)101,8996
Polymers101,8996
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: Coat protein
x 20


  • crystal asymmetric unit, crystal frame
  • 340 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)339,66320
Polymers339,66320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)175.470, 175.470, 418.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.521875, 0.849985, 0.07192), (-0.662108, 0.350474, 0.662406), (0.537829, -0.393312, 0.745685)
3generate(-0.251747, 0.713196, 0.654198), (-0.221329, -0.700482, 0.678483), (0.942145, 0.026013, 0.334195)
4generate(-0.251747, -0.22133, 0.942145), (0.713195, -0.700482, 0.026012), (0.654198, 0.678482, 0.334196)0.0001, -0.0001
5generate(0.521875, -0.662109, 0.537828), (0.849985, 0.350474, -0.393312), (0.071921, 0.662405, 0.745686)-0.0001
6generate(0.25461, -0.31217, 0.915272), (-0.312169, -0.922326, -0.227737), (0.915273, -0.227736, -0.332283)0.0001
7generate(0.831824, -0.252982, 0.494034), (0.325283, -0.499018, -0.803226), (0.449734, 0.828843, -0.332805)
8generate(0.867316, 0.424063, 0.260642), (0.068164, 0.417511, -0.906112), (-0.493069, 0.803651, 0.333207)0.0001
9generate(0.312035, 0.783313, 0.537638), (-0.728197, 0.56065, -0.394209), (-0.610216, -0.268499, 0.745348)
10generate(-0.066637, 0.328296, 0.942221), (-0.963256, -0.267415, 0.02505), (0.260188, -0.905931, 0.334053)
11generate(0.976614, -0.214999, 0.001122), (-0.214999, -0.976614, -0.000124), (0.001122, -0.00012, -0.999999)0.0001
12generate(0.652627, 0.754313, -0.071341), (0.534355, -0.524976, -0.662469), (-0.537162, 0.394223, -0.745684)
13generate(-0.197219, 0.847148, 0.493402), (0.270163, 0.530763, -0.803307), (-0.9424, -0.025128, -0.333544)-0.0001
14generate(-0.398461, -0.06479, 0.914894), (-0.642471, 0.731604, -0.228004), (-0.654568, -0.678644, -0.333141)
15generate(0.327006, -0.721232, 0.610648), (-0.942318, -0.200006, 0.268392), (-0.071439, -0.663191, -0.745033)-0.0001
16generate(0.316798, -0.106826, 0.942458), (0.250016, 0.967901, 0.025669), (-0.914949, 0.227498, 0.333337)
17generate(0.742939, -0.138848, 0.6548), (-0.496572, 0.541638, 0.678265), (-0.44884, -0.829065, 0.333456)
18generate(0.831823, 0.325285, 0.449733), (-0.252981, -0.499018, 0.828844), (0.494035, -0.803226, -0.332804)-0.0001, -0.0001
19generate(0.460615, 0.644156, 0.610653), (0.644155, -0.715917, 0.269309), (0.610654, 0.269308, -0.744698)0.0001, -0.0001, 0.0001
20generate(0.142312, 0.377097, 0.915175), (0.955024, 0.190689, -0.227081), (-0.260145, 0.906331, -0.332999)0.0001

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Components

#1: Protein Coat protein / Capsid protein


Mass: 16983.158 Da / Num. of mol.: 1 / Fragment: SPMV capsid protein / Source method: isolated from a natural source / Details: SPMV infected white perl millet leaves / Source: (natural) Satellite panicum mosaic virus / Plasmid details: SPMV infected white perl millet leaves / Tissue: white perl millet leaves / References: UniProt: Q86993

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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

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.45 %
Preparation: Matthews' Coefficient and solvent content calculated with the disordered RNA taken into account
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 6%-8% PEG 3350, pH 8.0-9.0 / PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 28, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 4.6→50 Å / Num. obs: 25998 / % possible obs: 97.4 % / Redundancy: 2.2 % / Rsym value: 0.167 / Net I/σ(I): 5.788
Reflection shellResolution: 4.6→4.76 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.98 / Rsym value: 0.462 / % possible all: 95.4

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data processing
X-PLORphasing
Omodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1STM

1stm


Resolution: 4.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.2935 2306 8.6 %RANDOM
Rwork0.2818 ---
obs0.2818 23224 87.1 %-
Solvent computationBsol: 58.18 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 126.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.995 Å20 Å20 Å2
2--5.995 Å20 Å2
3----11.99 Å2
Refinement stepCycle: LAST / Resolution: 4.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 0 0 1061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.791
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.813
X-RAY DIFFRACTIONc_mcangle_it1.526
X-RAY DIFFRACTIONc_scbond_it1.264
X-RAY DIFFRACTIONc_scangle_it2.148
LS refinement shellResolution: 4.6→4.76 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3592 194 -
Rwork0.3444 1929 -
obs--79.2 %
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:PROTEIN_REP.PARAM / Topol file: CNS_TOPPAR:PROTEIN.TOP

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