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- PDB-1x35: Recombinant T=3 capsid of a site specific mutant of SeMV CP -

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Basic information

Entry
Database: PDB / ID: 1x35
TitleRecombinant T=3 capsid of a site specific mutant of SeMV CP
ComponentsCoat protein
KeywordsVIRUS / T=3 capsids / beta-annulus / Icosahedral virus
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Viral coat protein subunit / viral capsid / structural molecule activity / metal ion binding / Capsid protein
Function and homology information
Biological speciesSesbania mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.1 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
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _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
B: Coat protein
C: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0966
Polymers85,9763
Non-polymers1203
Water00
1
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,165,768360
Polymers5,158,554180
Non-polymers7,214180
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
  • 430 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)430,48130
Polymers429,87915
Non-polymers60115
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
  • 517 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)516,57736
Polymers515,85518
Non-polymers72118
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 30


  • crystal asymmetric unit, crystal frame
  • 2.58 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,582,884180
Polymers2,579,27790
Non-polymers3,60790
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)471.500, 330.095, 351.474
Angle α, β, γ (deg.)90.00, 131.05, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)149.27166, 56.43043, -34.87592
3generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)258.49027, -46.89492, 28.98265
4generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)176.71943, -167.18392, 103.32534
5generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)16.96366, -138.20127, 85.41308
6generate(-1), (-1), (1)240.57801
7generate(-0.30901699, -0.80901699, 0.5), (0.80901699, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699)91.30635, -56.43043, -34.87592
8generate(0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5)-17.91226, 46.89492, 28.98265
9generate(0.80901699, 0.5, -0.30901699), (-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5)63.85858, 167.18392, 103.32534
10generate(-0.30901699, 0.80901699, -0.5), (-0.80901699, -0.5, -0.30901699), (-0.5, 0.30901699, 0.80901699)223.61435, 138.20127, 85.41308
11generate(-1), (-1), (1)252.597, 120.289, 132.308
12generate(-0.5, -0.30901699, -0.80901699), (-0.30901699, -0.80901699, 0.5), (-0.80901699, 0.5, 0.30901699)287.47292, -28.98265, 188.73843
13generate(-0.30901699, -0.80901699, -0.5), (0.80901699, -0.5, 0.30901699), (-0.5, -0.30901699, 0.80901699)223.61435, -138.20127, 85.41308
14generate(0.30901699, -0.80901699, -0.5), (0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.80901699)149.27166, -56.43043, -34.87592
15generate(0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699)167.18392, 103.32534, -5.89327
16generate(-1), (1), (-1)252.597, -120.289, 132.308
17generate(-0.5, -0.30901699, -0.80901699), (0.30901699, 0.80901699, -0.5), (0.80901699, -0.5, -0.30901699)287.47292, 28.98265, 75.87757
18generate(-0.30901699, -0.80901699, -0.5), (-0.80901699, 0.5, -0.30901699), (0.5, 0.30901699, -0.80901699)223.61435, 138.20127, 179.20291
19generate(0.30901699, -0.80901699, -0.5), (-0.80901699, -0.5, 0.30901699), (-0.5, 0.30901699, -0.80901699)149.27166, 56.43043, 299.49192
20generate(0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5), (-0.80901699, -0.5, -0.30901699)167.18392, -103.32534, 270.50926
21generate(-1), (1), (-1)120.289, -132.308, 252.597
22generate(0.80901699, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699), (-0.30901699, -0.80901699, 0.5)63.85858, -167.18392, 103.32534
23generate(0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699)167.18392, -103.32534, -5.89327
24generate(-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5), (0.80901699, 0.5, -0.30901699)287.47292, -28.98265, 75.87757
25generate(-0.80901699, -0.5, -0.30901699), (-0.5, 0.30901699, 0.80901699), (-0.30901699, 0.80901699, -0.5)258.49027, -46.89492, 235.63334
26generate(-1), (-1), (1)120.289, 132.308, 12.01899
27generate(0.80901699, -0.5, -0.30901699), (-0.5, -0.30901699, -0.80901699), (0.30901699, 0.80901699, -0.5)63.85858, 167.18392, 161.29065
28generate(0.5, 0.30901699, -0.80901699), (-0.30901699, -0.80901699, -0.5), (-0.80901699, 0.5, -0.30901699)167.18392, 103.32534, 270.50926
29generate(-0.5, 0.30901699, -0.80901699), (0.30901699, -0.80901699, -0.5), (-0.80901699, -0.5, 0.30901699)287.47292, 28.98265, 188.73843
30generate(-0.80901699, -0.5, -0.30901699), (0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5)258.49027, 46.89492, 28.98265

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Components

#1: Protein Coat protein


Mass: 28658.633 Da / Num. of mol.: 3 / Mutation: P53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EB06
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 2004
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4.1→20 Å / Num. all: 352930 / Num. obs: 324695 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 4.1→4.25 Å / % possible all: 74.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 29326465.94 / 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
Rfree0.27 14626 4.9 %RANDOM
Rwork0.268 ---
all0.268 301529 --
obs-297206 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.492238 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å27.2 Å2
2---2.66 Å20 Å2
3---4.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.55 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 4.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4439 0 3 0 4442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d3.32
X-RAY DIFFRACTIONc_mcbond_it11.61.5
X-RAY DIFFRACTIONc_mcangle_it17.992
X-RAY DIFFRACTIONc_scbond_it25.62
X-RAY DIFFRACTIONc_scangle_it33.242.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 4.1→4.35 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 2264 4.9 %
Rwork0.302 44141 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top

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