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

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Basic information

Entry
Database: PDB / ID: 5cvz
TitleInvestigation of RNA structure in satellite panicum mosaic virus - glutaraldehyde treated
ComponentsCoat protein
KeywordsVIRUS / capsid protein / satellite virus / glutaraldehyde cross-linked
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Potexvirus coat protein / Satellite virus coat / Satellite virus coat domain / Satellite virus coat domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPanicum mosaic satellite virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.2Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Coat protein


Theoretical massNumber of molelcules
Total (without water)15,1081
Polymers15,1081
Non-polymers00
Water0
1
A: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)906,47760
Polymers906,47760
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
  • 75.5 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)75,5405
Polymers75,5405
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
x 6


  • icosahedral 23 hexamer
  • 90.6 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)90,6486
Polymers90,6486
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
  • 302 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)302,15920
Polymers302,15920
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)226.350, 226.350, 226.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.935851, 0.352379, -0.003547), (-0.120857, 0.330396, 0.936073), (0.331024, -0.875596, 0.351788)-0.848, -0.4338, 3.5533
3generate(0.832054, 0.449305, 0.325287), (0.156828, -0.753048, 0.639002), (0.532064, -0.48067, -0.69704)-1.8072, 2.8515, 4.9024
4generate(0.832053, 0.156827, 0.532064), (0.449305, -0.753047, -0.480671), (0.325288, 0.639003, -0.697039)-1.5519, 5.3157, 2.1828
5generate(0.93585, -0.120858, 0.331026), (0.352381, 0.330396, -0.875595), (-0.003547, 0.936072, 0.351789)-0.435, 3.5533, -0.8469
6generate(0.356452, -0.497822, 0.790642), (-0.497821, -0.817298, -0.290169), (0.790643, -0.290167, -0.539154)1.0449, 7.7612, 3.0942
7generate(0.655474, -0.731155, -0.189122), (-0.463163, -0.191385, -0.865362), (0.596519, 0.654817, -0.464091)3.7679, 7.5069, 0.6339
8generate(0.639188, 0.155001, -0.753268), (-0.696776, 0.531266, -0.481933), (0.325486, 0.832905, 0.44758)2.857, 4.9078, -1.8052
9generate(0.3301, 0.936007, -0.122166), (-0.875818, 0.351975, 0.330237), (0.352104, -0.002016, 0.935959)-0.4288, 3.5558, -0.8521
10generate(0.155361, 0.532542, 0.832023), (-0.752856, -0.481483, 0.448755), (0.639586, -0.696112, 0.326124)-1.5489, 5.3192, 2.1758
11generate(-0.102159, -0.990263, 0.094569), (-0.990263, 0.092198, -0.104303), (0.094569, -0.104304, -0.990039)5.9516, 5.9651, 5.9574
12generate(0.05538, -0.445981, -0.893327), (-0.972408, -0.227159, 0.053123), (-0.226619, 0.865737, -0.446255)6.8038, 6.3942, 2.4045
13generate(-0.189987, 0.654359, -0.731929), (-0.864989, -0.464224, -0.1905), (-0.464434, 0.596918, 0.654209)3.7761, 7.5062, 0.6354
14generate(-0.49917, 0.790123, 0.355717), (-0.816455, -0.29138, -0.498496), (-0.290224, -0.539261, 0.790549)1.0526, 7.7643, 3.095
15generate(-0.44489, -0.226308, 0.866521), (-0.893879, 0.052507, -0.445223), (0.055259, -0.97264, -0.225651)2.3971, 6.8118, 6.384
16generate(0.531329, 0.832757, 0.155584), (-0.481346, 0.447885, -0.753462), (-0.697134, 0.325446, 0.638818)-1.5481, 5.3233, 2.1833
17generate(0.448103, 0.326141, 0.832368), (-0.754013, 0.638091, 0.155902), (-0.48028, -0.697476, 0.531844)-1.8072, 2.8598, 4.903
18generate(0.655473, -0.463163, 0.596519), (-0.731155, -0.191385, 0.654816), (-0.189121, -0.865362, -0.464092)0.6291, 3.7766, 7.5028
19generate(0.866865, -0.44436, -0.226028), (-0.44436, -0.894231, 0.053799), (-0.226028, 0.053801, -0.972634)2.3937, 6.8064, 6.3895
20generate(0.79014, 0.356562, -0.498541), (-0.28997, -0.49914, -0.816564), (-0.539997, 0.789762, -0.290998)1.0481, 7.7623, 3.1018

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Components

#1: Protein Coat protein / Capsid protein


Mass: 15107.958 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) Panicum mosaic satellite 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: 2.25 Å3/Da / Density % sol: 45.43 %
Preparation: Matthews' coeficient and solvent content include correction for disordered RNA
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 6%-14% PEG 3350, pH 5.0-7.0. Gluteraldehyde-treated before freezing
PH range: 5.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→100 Å / Num. obs: 58624 / % possible obs: 100 % / Redundancy: 17.2 % / Rsym value: 0.123 / Net I/σ(I): 27.725
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 13 % / Mean I/σ(I) obs: 6.48 / Rsym value: 0.44 / % possible all: 100

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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: 3.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: RESIDUAL
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5164 8.9 %RANDOM
Rwork0.23 ---
obs0.23 50688 87.6 %-
Solvent computationBsol: 45.45 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 67.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 0 0 1061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.549
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_it1.026
X-RAY DIFFRACTIONc_mcangle_it1.805
X-RAY DIFFRACTIONc_scbond_it1.859
X-RAY DIFFRACTIONc_scangle_it3.041
LS refinement shellResolution: 3.3→3.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2971 352 -
Rwork0.2922 3660 -
obs--70.7 %
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:PROTEIN_REP.PARAM / Topol file: CNS_TOPPAR:PROTEIN.TOP

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