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- PDB-1laj: The Structure of Tomato Aspermy Virus by X-Ray Crystallography -

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Basic information

Entry
Database: PDB / ID: 1laj
TitleThe Structure of Tomato Aspermy Virus by X-Ray Crystallography
Components
  • 5'-R(*AP*AP*A)-3'
  • capsid protein
KeywordsVirus/RNA / anti-parallel beta sheets / jelly roll / T=3 icosahedral virus / protein-RNA complex / disulphide bridge / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


T=3 icosahedral viral capsid / viral nucleocapsid / structural molecule activity / RNA binding
Similarity search - Function
Cucumovirus coat protein, subunit A / Cucumovirus coat protein, chain A / Cucumovirus coat protein / Cucumovirus coat protein, subunit A superfamily / Cucumovirus coat protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / RNA / Capsid protein
Similarity search - Component
Biological speciesTomato aspermy virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLucas, R.W. / Larson, S.B. / Canady, M.A. / McPherson, A.
Citation
Journal: J.STRUCT.BIOL. / Year: 2002
Title: The Structure of Tomato Aspermy Virus by X-Ray Crystallography
Authors: Lucas, R.W. / Larson, S.B. / Canady, M.A. / McPherson, A.
#1: Journal: Proteins / Year: 1995
Title: Preliminary X-ray Diffraction Analysis of Crystals of Tomato aspermy virus (TAV)
Authors: Canady, M.A. / Leja, C.A. / Day, J. / McPherson, A.
History
DepositionMar 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_site
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 / _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
R: 5'-R(*AP*AP*A)-3'
A: capsid protein
B: capsid protein
C: capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4506
Polymers73,3314
Non-polymers1192
Water00
1
R: 5'-R(*AP*AP*A)-3'
A: capsid protein
B: capsid protein
C: capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,407,027360
Polymers4,399,870240
Non-polymers7,157120
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
R: 5'-R(*AP*AP*A)-3'
A: capsid protein
B: capsid protein
C: capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 367 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)367,25230
Polymers366,65620
Non-polymers59610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: 5'-R(*AP*AP*A)-3'
A: capsid protein
B: capsid protein
C: capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 441 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)440,70336
Polymers439,98724
Non-polymers71612
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
R: 5'-R(*AP*AP*A)-3'
A: capsid protein
B: capsid protein
C: capsid protein
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.1 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,101,75790
Polymers1,099,96760
Non-polymers1,78930
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)294.296, 327.393, 382.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
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)
6generate(0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5)
7generate(0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699)
8generate(0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699)
9generate(0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5)
10generate(1), (1), (1)
11generate(-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699)
12generate(-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.30901699)
13generate(1), (1), (1)
14generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)
15generate(0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699)

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Components

#1: RNA chain 5'-R(*AP*AP*A)-3'


Mass: 942.660 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein capsid protein


Mass: 24129.502 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tomato aspermy virus / Genus: Cucumovirus / Strain: Blencowe / References: UniProt: P23627
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 33

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 14-17% Ethanol, 100mM tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1droppH8.5
214-17 %ethanol1drop
3100 mMTris1drop
4100 mMTris1reservoirpH8.5
520 %MPD1reservoir
610 %ethanol1reservoir
70.04 %sodium azide1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12B11.15
SYNCHROTRONSSRL BL7-121.08
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEApr 1, 1997
MARRESEARCH2IMAGE PLATEApr 23, 1997
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.151
21.081
ReflectionResolution: 3.4→49.72 Å / Num. all: 156531 / Num. obs: 156468 / % possible obs: 62.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.522 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.9
Reflection shellResolution: 3.4→3.46 Å / Num. unique all: 269 / % possible all: 2.2
Reflection
*PLUS
% possible obs: 62 % / Num. measured all: 1444765 / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F15

1f15


Resolution: 3.4→50 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: NCS RESTRAINTS WERE USED FOR BETA STRANDS AND HELICES OF EQUIVALENT SUBUNITS. IONS WERE FIXED AS RNA PHOSPHATES. ICOSAHEDRAL NCS CONSTRAINTS WERE APPLIED THROUGHOUT REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 6391 5 %RANDOM
Rwork0.218 ---
all0.278 156468 --
obs-127436 50.8 %-
Displacement parametersBiso mean: 105 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.55 Å
Luzzati d res low-5 Å
Luzzati sigma a1.69 Å1.61 Å
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 63 6 0 4308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.03
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it7.51.5
X-RAY DIFFRACTIONx_mcangle_it12.252
X-RAY DIFFRACTIONx_scbond_it16.252
X-RAY DIFFRACTIONx_scangle_it22.852.5
Refine LS restraints NCSNCS model details: CONSTRAINTS / Rms dev position: 0.059 Å / Weight Biso : 4 / Weight position: 100
LS refinement shellResolution: 3.4→3.52 Å / Rfactor Rfree error: 0.088 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.488 30 4.942 %
Rwork0.402 607 -
obs--2.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PO4_XPLOR_PAR.TXTPO4_XPLOR_TOP.TXT
X-RAY DIFFRACTION4MG_XPLOR_PAR.TXTMG_XPLOR_TOP.TXT
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.03

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