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- PDB-1x33: T=3 recombinant capsid of SeMV CP -

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Basic information

Entry
Database: PDB / ID: 1x33
TitleT=3 recombinant capsid of SeMV CP
ComponentsCoat protein
KeywordsVIRUS / T=3 capsids / recombinant CP / Icosahedral virus
Function / homology
Function and homology information


viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSesbania mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Saravanan, V. / Vijay, C.S. / Savithri, H.S. / Murthy, M.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structural studies on recombinant T = 3 capsids of Sesbania mosaic virus coat protein mutants.
Authors: Sangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Saravanan, V. / Vijay, C.S. / Savithri, H.S. / Murthy, M.R.
History
DepositionApr 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)86,1746
Polymers86,0543
Non-polymers1203
Water0
1
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,170,455360
Polymers5,163,241180
Non-polymers7,214180
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 5


  • icosahedral pentamer
  • 431 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)430,87130
Polymers430,27015
Non-polymers60115
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 517 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)517,04636
Polymers516,32418
Non-polymers72118
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
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 20


  • crystal asymmetric unit, crystal frame
  • 1.72 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,723,485120
Polymers1,721,08060
Non-polymers2,40560
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation20
Unit cell
Length a, b, c (Å)291.315, 291.315, 291.315
Angle α, β, γ (deg.)61.63, 61.63, 61.63
Int Tables number146
Space group name H-MR3
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.64873213, 0.56952246, 0.50476805), (0.07349464, 0.61329472, -0.78642745), (-0.75745967, 0.5472785, 0.35600714)
3generate(0.08036878, 0.99500134, 0.05927219), (0.68843929, -0.01240758, -0.72518784), (-0.72082745, 0.09908777, -0.68599519)
4generate(0.08036878, 0.68843929, -0.72082745), (0.99500134, -0.01240758, 0.09908777), (0.05927219, -0.72518784, -0.68599519)
5generate(0.64873213, 0.07349464, -0.75745967), (0.56952246, 0.61329472, 0.5472785), (0.50476805, -0.78642745, 0.35600714)
6generate(-0.71443027, 0.02216066, -0.69935563), (0.02216066, -0.9982803, -0.05427109), (-0.69935563, -0.05427109, 0.71271057)
7generate(0.06788851, -0.77603537, -0.62702492), (-0.01788376, -0.62932044, 0.77694012), (-0.99753262, -0.04153174, -0.05660206)
8generate(0.46195311, -0.78043162, 0.42133812), (-0.64635426, 0.02905852, 0.76248395), (-0.60731005, -0.62456552, -0.49101163)
9generate(-0.07682035, 0.01504737, 0.9969314), (-0.99472598, 0.06699924, -0.07766167), (-0.06796225, -0.99763955, 0.00982111)
10generate(-0.80386526, 0.51107668, 0.30430457), (-0.58156103, -0.56793107, -0.58244404), (-0.12484955, -0.64517821, 0.75376234)
11generate(-0.07146419, 0.77035753, 0.63359462), (-0.69100538, -0.49632658, 0.52552021), (0.71930831, -0.40026141, 0.56779077)
12generate(-0.46966634, 0.77850845, -0.41633894), (-0.8828151, -0.41033164, 0.22861636), (0.00714273, 0.47492371, 0.87999798)
13generate(0.06788851, -0.01788376, -0.99753262), (-0.77603537, -0.62932044, -0.04153174), (-0.62702492, 0.77694012, -0.05660206)
14generate(0.79831783, -0.51823214, -0.30679651), (-0.51823214, -0.8506579, 0.08841141), (-0.30679651, 0.08841141, -0.94765992)
15generate(0.71219312, -0.03107223, 0.70129557), (-0.46568072, -0.76846318, 0.43886879), (0.52528319, -0.63913915, -0.56176393)
16generate(-0.46730926, -0.28144059, -0.83810098), (0.64919572, 0.5342673, -0.54139022), (0.60013913, -0.79708823, -0.06695803)
17generate(0.31098478, -0.89742379, -0.31292012), (0.87050117, 0.40110362, -0.285208), (0.38146583, -0.18370198, 0.90594558)
18generate(0.37281435, -0.5445269, 0.75133209), (0.8102346, 0.5856765, 0.0224262), (-0.45224921, 0.60039445, 0.65954314)
19generate(-0.36726692, 0.28955858, 0.88389527), (0.55168236, 0.83291248, -0.04362764), (-0.74884016, 0.47160644, -0.46564556)
20generate(-0.88649187, 0.45215486, -0.09842839), (0.45215486, 0.80113985, -0.39208536), (-0.09842839, -0.39208536, -0.91464798)

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Components

#1: Protein Coat protein


Mass: 28684.672 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Plasmid: pSBET A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q9EB06
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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: 1

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Sample preparation

Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 6% PEG 3350, 0.1M MgCl2, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 13, 2003
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.6→18 Å / Num. all: 191916 / Num. obs: 191916 / % possible obs: 76 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.6→3.73 Å / % possible all: 62.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 232241.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 15788 9.9 %RANDOM
Rwork0.232 ---
obs0.232 159147 59.1 %-
all-191916 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.256334 e/Å3
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å2-6.53 Å2-7.26 Å2
2---1.41 Å2-4.08 Å2
3----1.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.83 Å
Refinement stepCycle: LAST / Resolution: 3.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4526 0 3 0 4529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.92
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.6→3.82 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 1358 9.9 %
Rwork0.334 12310 -
obs--30.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top

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