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- PDB-2buk: SATELLITE TOBACCO NECROSIS VIRUS -

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Basic information

Entry
Database: PDB / ID: 2buk
TitleSATELLITE TOBACCO NECROSIS VIRUS
ComponentsCOAT PROTEIN
KeywordsVIRUS / CAPSID / TOBACCO NECROSIS SATELLITE VIRUS / VIRUS/VIRAL PROTEIN / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


viral capsid / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Satellite tobacco necrosis virus coat protein-like / Satellite tobacco necrosis virus coat protein / Satellite virus coat / Satellite virus coat domain superfamily / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTOBACCO NECROSIS VIRUS
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.45 Å
AuthorsJones, T.A. / Liljas, L.
Citation
Journal: J.Mol.Biol. / Year: 1984
Title: Structure of Satellite Tobacco Necrosis Virus After Crystallographic Refinement at 2.5 A Resolution.
Authors: Jones, T.A. / Liljas, L.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1984
Title: Crystallographic Refinement of Macromolecules Having Non-Crystallographic Symmetry
Authors: Jones, T.A. / Liljas, L.
#2: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Satellite Tobacco Necrosis Virus at 3.0 Angstroms Resolution
Authors: Liljas, L. / Unge, T. / Jones, T.A. / Fridborg, K. / Lovgren, S. / Skoglund, U. / Strandberg, B.
History
DepositionJun 14, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionAug 18, 2005ID: 2STV
Revision 1.0Aug 18, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Derived calculations / Other / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8604
Polymers21,7401
Non-polymers1203
Water2,846158
1
A: COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,311,593240
Polymers1,304,37960
Non-polymers7,214180
Water1,08160
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
hetero molecules
x 5


  • icosahedral pentamer
  • 109 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)109,29920
Polymers108,6985
Non-polymers60115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 131 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)131,15924
Polymers130,4386
Non-polymers72118
Water1086
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
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 1.31 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,311,593240
Polymers1,304,37960
Non-polymers7,214180
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)317.270, 304.030, 184.600
Angle α, β, γ (deg.)90.00, 94.36, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.600223, 0.189076, 0.777164), (-0.719961, 0.550976, 0.421997), (-0.348409, -0.81282, 0.466836)-6.37893, 33.78484, 50.49749
3generate(-0.046631, -0.41403, 0.909068), (-0.975846, -0.17556, -0.130014), (0.213426, -0.893173, -0.395843)35.425, 78.30184, 48.833
4generate(-0.046631, -0.975846, 0.213426), (-0.41403, -0.17556, -0.893173), (0.909068, -0.130014, -0.395843)67.64018, 72.03002, -2.6932
5generate(0.600223, -0.719961, -0.348409), (0.189076, 0.550976, -0.81282), (0.777164, 0.421997, 0.466836)45.74632, 23.63682, -32.87365
6generate(-0.889091, -0.241159, 0.389049), (-0.241159, -0.475628, -0.845944), (0.389049, -0.845944, 0.364719)121.90811, 57.03826, 0.60297
7generate(-0.495576, -0.617205, -0.611115), (0.492419, 0.379943, -0.78305), (0.715491, -0.688985, 0.115633)139.07806, -0.21044, -12.04143
8generate(0.359826, 0.06296, -0.930893), (0.294838, 0.938922, 0.177469), (0.885209, -0.338321, 0.319286)90.52733, -30.05729, -34.04358
9generate(0.494978, 0.859372, -0.128361), (-0.560851, 0.42882, 0.708209), (0.663659, -0.278557, 0.694236)43.35137, 8.74506, -34.99726
10generate(-0.276895, 0.671416, 0.687408), (-0.892115, -0.44542, 0.075705), (0.357015, -0.592285, 0.722315)62.74576, 62.57307, -13.58452
11generate(0.457914, -0.507275, -0.73006), (-0.507275, -0.823496, 0.254021), (-0.73006, 0.254021, -0.634418)73.9614, 25.81012, 129.76542
12generate(0.894428, 0.400491, -0.199013), (0.199904, -0.756113, -0.623162), (-0.400047, 0.51759, -0.756348)17.03601, 14.05174, 110.96798
13generate(0.317855, 0.551537, 0.771217), (0.881474, 0.127715, -0.454634), (-0.349244, 0.824315, -0.445571)14.81143, -44.23672, 92.81286
14generate(-0.475, -0.262878, 0.839804), (0.595529, 0.606569, 0.526706), (-0.647858, 0.750313, -0.131569)70.36194, -68.5026, 100.38982
15generate(-0.388439, -0.917259, -0.088036), (-0.262765, 0.018688, 0.964679), (-0.883215, 0.397852, -0.248283)106.91863, -25.21127, 123.22776
16generate(-0.568823, 0.748434, 0.34101), (0.748434, 0.299124, 0.591922), (0.34101, 0.591922, -0.730301)100.41051, -82.84841, 54.87161
17generate(-0.999074, 0.027638, 0.032964), (0.027638, -0.174805, 0.984215), (0.032964, 0.984215, 0.17388)146.54486, -47.62617, 35.81597
18generate(-0.631051, -0.200467, -0.749392), (-0.200467, -0.891077, 0.407179), (-0.749392, 0.407179, 0.522128)155.51626, -4.00786, 77.63773
19generate(0.026652, 0.379352, -0.924869), (0.379352, -0.859828, -0.341742), (-0.924869, -0.341742, -0.166824)114.92653, -12.27251, 122.54065
20generate(0.065111, 0.965804, -0.250963), (0.965804, -0.124244, -0.227564), (-0.250963, -0.227564, -0.940868)80.8693, -60.99864, 108.47042
21generate(0.706825, 0.38041, 0.596395), (-0.385319, -0.499995, 0.775587), (0.593235, -0.778006, -0.20683)-5.90357, -7.37689, 11.94737
22generate(-0.057417, -0.141521, 0.988269), (-0.141521, -0.978752, -0.14838), (0.988269, -0.14838, 0.036169)32.55616, 17.35396, -28.56605
23generate(-0.276895, -0.892115, 0.357015), (0.671416, -0.44542, -0.592285), (0.687408, 0.075705, 0.722315)78.04624, -22.3031, -38.05672
24generate(0.351703, -0.834077, -0.424995), (0.930042, 0.362953, 0.057335), (0.106432, -0.415428, 0.903378)67.70092, -71.54336, -3.40886
25generate(0.959675, -0.047613, -0.27705), (0.276944, 0.329224, 0.902726), (0.04823, -0.943051, 0.329135)15.81708, -62.31845, 27.49537
26generate(-0.488144, -0.855907, 0.170701), (0.764903, -0.325368, 0.555931), (-0.420284, 0.401944, 0.813512)102.32166, -82.40153, 39.76672
27generate(0.263751, -0.70263, -0.660869), (0.499673, -0.486517, 0.716679), (-0.825083, -0.519243, 0.222766)85.1388, -70.20019, 97.10762
28generate(0.894428, 0.199904, -0.400047), (0.400491, -0.756113, 0.51759), (-0.199013, -0.623162, -0.756348)26.34592, -53.63399, 96.07735
29generate(0.532313, 0.604423, 0.592719), (0.604423, -0.761584, 0.233799), (0.592719, 0.233799, -0.770728)7.19279, -55.59686, 38.0997
30generate(-0.322164, -0.048104, 0.945461), (0.829642, -0.495369, 0.257495), (0.455966, 0.86735, 0.199499)54.14838, -73.37618, 3.29782
31generate(-0.304711, -0.520324, -0.797756), (-0.489032, 0.804222, -0.33775), (0.817312, 0.287212, -0.49951)133.58404, 51.86382, 8.90405
32generate(0.469663, 0.304132, -0.828806), (-0.754862, 0.625172, -0.198353), (0.457821, 0.718793, 0.523198)77.66405, 65.0983, -11.83013
33generate(0.351703, 0.930042, 0.106432), (-0.834077, 0.362953, -0.415428), (-0.424995, 0.057335, 0.903378)43.09053, 81.01855, 35.95397
34generate(-0.495576, 0.492419, 0.715491), (-0.617205, 0.379943, -0.688985), (-0.611115, -0.78305, 0.115633)77.64291, 77.62332, 86.22034
35generate(-0.901262, -0.403956, 0.156673), (-0.403956, 0.652662, -0.640978), (0.156673, -0.640978, -0.7514)133.57097, 59.6047, 69.50257
36generate(0.08603, 0.995821, 0.03066), (0.109448, 0.021141, -0.993768), (-0.990263, 0.08885, -0.107172)66.27789, 37.91457, 124.62187
37generate(-0.675997, 0.540018, 0.501406), (0.39671, 0.840096, -0.369946), (-0.621007, -0.05117, -0.782133)100.921, -12.2521, 128.52856
38generate(-0.969235, -0.23783, -0.0634), (-0.23783, 0.83858, 0.490123), (-0.0634, 0.490123, -0.869345)148.79732, -5.08148, 91.2654
39generate(-0.388439, -0.262765, -0.883215), (-0.917259, 0.018688, 0.397852), (-0.088036, 0.964679, -0.248283)143.7434, 49.51688, 64.32881
40generate(0.263751, 0.499673, -0.825083), (-0.70263, -0.486517, -0.519243), (-0.660869, 0.716679, 0.222766)92.74358, 76.0899, 84.94425
41generate(0.706825, -0.385319, 0.593235), (0.38041, -0.499995, -0.778006), (0.596395, 0.775587, -0.20683)-5.75726, 7.85249, 11.71335
42generate(0.494978, -0.560851, 0.663659), (0.859372, 0.42882, -0.278557), (-0.128361, 0.708209, 0.694236)6.67292, -50.75371, 23.66766
43generate(0.469663, -0.754862, 0.457821), (0.304132, 0.625172, 0.718793), (-0.828806, -0.198353, 0.523198)18.08033, -55.81439, 83.47036
44generate(0.665865, -0.699235, 0.260183), (-0.517986, -0.18229, 0.835739), (-0.536949, -0.691261, -0.483575)12.70032, -0.33584, 108.47615
45generate(0.812439, -0.470844, 0.343874), (-0.470844, -0.877682, -0.089333), (0.343874, -0.089333, -0.934757)-2.03212, 39.01245, 64.12788
46generate(-0.304711, -0.489032, 0.817312), (-0.520324, 0.804222, 0.287212), (-0.797756, -0.33775, -0.49951)58.79026, 25.23957, 128.5321
47generate(-0.115569, -0.991386, -0.06163), (-0.991386, 0.111274, 0.069083), (-0.06163, 0.069083, -0.995705)85.4843, 70.23268, 96.98609
48generate(0.665865, -0.517986, -0.536949), (-0.699235, -0.18229, -0.691261), (0.260183, 0.835739, -0.483575)49.61551, 83.80458, 49.43258
49generate(0.959675, 0.276944, 0.04823), (-0.047613, 0.329224, -0.943051), (-0.27705, 0.902726, 0.329135)0.75334, 47.19938, 51.58891
50generate(0.359826, 0.294838, 0.885209), (0.06296, 0.938922, -0.338321), (-0.930893, 0.177469, 0.319286)6.42364, 11.00421, 100.47511
51generate(0.08603, 0.109448, -0.990263), (0.995821, 0.021141, 0.08885), (0.03066, -0.993768, -0.107172)113.55681, -77.87507, 49.00213
52generate(0.317855, 0.881474, -0.349244), (0.551537, 0.127715, 0.824315), (0.771217, -0.454634, -0.445571)66.69993, -79.0264, 9.82037
53generate(-0.322164, 0.829642, 0.455966), (-0.048104, -0.495369, 0.86735), (0.945461, 0.257495, 0.199499)76.81691, -36.60392, -32.9591
54generate(-0.949542, 0.025581, 0.312593), (0.025581, -0.987031, 0.158481), (0.312593, 0.158481, 0.936573)129.92641, -9.23406, -20.2165
55generate(-0.697265, -0.419523, -0.581225), (0.670762, -0.667809, -0.322659), (-0.252785, -0.614842, 0.74704)152.63292, -34.74104, 30.43832
56generate(-0.488144, 0.764903, -0.420284), (-0.855907, -0.325368, 0.401944), (0.170701, 0.555931, 0.813512)129.69021, 44.78298, -4.00758
57generate(-0.697265, 0.670762, -0.252785), (-0.419523, -0.667809, -0.614842), (-0.581225, -0.322659, 0.74704)137.42286, 59.54741, 54.76589
58generate(-0.813364, 0.443206, -0.376838), (0.443206, 0.052487, -0.894882), (-0.376838, -0.894882, -0.239123)151.76727, 8.61369, 85.29616
59generate(-0.675997, 0.39671, -0.621007), (0.540018, 0.840096, -0.05117), (0.501406, -0.369946, -0.782133)152.89994, -37.6295, 45.39144
60generate(-0.475, 0.595529, -0.647858), (-0.262878, 0.606569, 0.750313), (0.839804, 0.526706, -0.131569)139.25557, -15.27565, -9.80131

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Components

#1: Protein COAT PROTEIN / SATELLITE TOBACCO NECROSIS VIRUS 1


Mass: 21739.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TOBACCO NECROSIS VIRUS / References: UniProt: P03606
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 100

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Sample preparation

CrystalDescription: NONE
Crystal grow
*PLUS
pH: 6.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-12 g/lvirus11
21 mM11MgCl2
350 mMsodium phosphate11

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-6 / Wavelength: 1.5418
DetectorDetector: FILM / Date: Jan 1, 1981 / Details: BENT MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→24.73 Å / Num. obs: 503000 / % possible obs: 76 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.14

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Processing

Software
NameVersionClassification
FRODOrefinement
FILMEdata reduction
PURDUEDATA PROCESSING PACKAGEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.45→7.5 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.273 -
obs-485000
Refinement stepCycle: LAST / Resolution: 2.45→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 3 158 1588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.4
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d29.7
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d2.06
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: FRODO / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg29.7
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg2.06

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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