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- PDB-2mev: STRUCTURAL REFINEMENT AND ANALYSIS OF MENGO VIRUS -

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Basic information

Entry
Database: PDB / ID: 2mev
TitleSTRUCTURAL REFINEMENT AND ANALYSIS OF MENGO VIRUS
Components(MENGO VIRUS COAT PROTEIN (SUBUNIT ...) x 4
KeywordsVIRUS / CARDIO PICORNAVIRUS COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase ...positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 ...Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesMengo virus
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsRossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Structural refinement and analysis of Mengo virus.
Authors: Krishnaswamy, S. / Rossmann, M.G.
#1: Journal: Science / Year: 1987
Title: The Atomic Structure of Mengo Virus at 3.0 Angstroms Resolution
Authors: Luo, M. / Vriend, G. / Kamer, G. / Minor, I. / Arnold, E. / Rossmann, M.G. / Boege, U. / Scraba, D.G. / Duke, G.M. / Palmenberg, A.C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Implications of the Picornavirus Capsid Structure for Polyprotein Processing
Authors: Arnold, E. / Luo, M. / Vriend, G. / Rossmann, M.G. / Palmenberg, A.C. / Parks, G.D. / Nicklin, M.J.H. / Wimmer, E.
#3: Journal: Chem.Scr. / Year: 1986
Title: The Structure of a Human Common Cold Virus (Rhinovirus 14) and its Evolutionary Relations to Other Viruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Vriend, G. / Mosser, A.G. / Palmenberg, A.C. / ...Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Vriend, G. / Mosser, A.G. / Palmenberg, A.C. / Rueckert, R.R. / Sherry, B.
#4: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G.
#5: Journal: J.Mol.Biol. / Year: 1984
Title: Picornaviruses of Two Different Genera Have Similar Structures
Authors: Luo, M. / Arnold, E. / Erickson, J.W. / Rossmann, M.G. / Boege, U. / Scraba, D.G.
History
DepositionApr 21, 1989Processing site: BNL
SupersessionJan 15, 1990ID: 1MEV
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_angle.linker_flag / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)
2: MENGO VIRUS COAT PROTEIN (SUBUNIT VP2)
3: MENGO VIRUS COAT PROTEIN (SUBUNIT VP3)
4: MENGO VIRUS COAT PROTEIN (SUBUNIT VP4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9395
Polymers91,8444
Non-polymers951
Water4,197233
1
1: MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)
2: MENGO VIRUS COAT PROTEIN (SUBUNIT VP2)
3: MENGO VIRUS COAT PROTEIN (SUBUNIT VP3)
4: MENGO VIRUS COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,516,336300
Polymers5,510,637240
Non-polymers5,69860
Water4,324240
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
1: MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)
2: MENGO VIRUS COAT PROTEIN (SUBUNIT VP2)
3: MENGO VIRUS COAT PROTEIN (SUBUNIT VP3)
4: MENGO VIRUS COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 5


  • icosahedral pentamer
  • 460 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)459,69525
Polymers459,22020
Non-polymers4755
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)
2: MENGO VIRUS COAT PROTEIN (SUBUNIT VP2)
3: MENGO VIRUS COAT PROTEIN (SUBUNIT VP3)
4: MENGO VIRUS COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 552 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)551,63430
Polymers551,06424
Non-polymers5706
Water43224
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
1: MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)
2: MENGO VIRUS COAT PROTEIN (SUBUNIT VP2)
3: MENGO VIRUS COAT PROTEIN (SUBUNIT VP3)
4: MENGO VIRUS COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 5.52 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)5,516,336300
Polymers5,510,637240
Non-polymers5,69860
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)441.420, 427.310, 421.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO 1 105, PRO 2 85, PRO 2 152, PRO 3 59 ARE CIS PROLINES.
2: SEE REMARK 9. / 3: SEE REMARK 10.
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.9860209, -0.13965473, 0.09088525), (0.13060843, 0.30904694, -0.94204293), (0.10346934, 0.94072987, 0.32296614)7.21568, 158.72985, -42.8753
3generate(0.96340098, -0.09536389, 0.25052838), (0.07167422, -0.808938, -0.58351307), (0.25830728, 0.5801036, -0.77249696)-11.73363, 249.11763, 93.34593
4generate(0.96340019, 0.07166411, 0.258308), (-0.09535757, -0.80893764, 0.58011349), (0.25053305, -0.58350556, -0.77249653)-30.66061, 146.2505, 220.41059
5generate(0.98601962, 0.13060223, 0.10347295), (-0.13965466, 0.30904753, 0.94074441), (0.09089037, -0.94202931, 0.32296683)-23.40883, -7.71266, 162.71963
6generate(0.17738858, -0.01897243, 0.98395586), (-0.01896687, -0.99969437, -0.01585081), (0.98396024, -0.01585552, -0.17769421)-9.17711, 220.64168, 15.23557
7generate(0.27424016, 0.89500015, 0.35177927), (-0.15091032, -0.321215, 0.93491193), (0.94974859, -0.30947706, 0.04697484)-53.09603, 62.5031, 27.43746
8generate(0.42369946, 0.56922739, -0.70459138), (-0.0940194, 0.80130441, 0.5908277), (0.90091212, -0.1840892, 0.39303011)75.86339, -29.65686, -16.84677
9generate(0.41921882, -0.54608382, -0.72528776), (0.07308458, 0.8165802, -0.57259079), (0.90494115, 0.18702632, 0.38223496)199.48362, 71.52373, -56.41782
10generate(0.26699032, -0.9096113, 0.31829183), (0.11946959, -0.29649826, -0.94753873), (0.95626771, 0.29100044, 0.02950794)146.9257, 226.21674, -36.58984
11generate(-0.17743328, 0.00951345, -0.9840847), (0.00951716, -0.99988993, -0.01138592), (-0.98408896, -0.01138154, 0.17732321)232.56461, 217.03032, 196.49184
12generate(-0.27553299, -0.89803838, -0.34291418), (-0.12238803, -0.32105312, 0.93912694), (-0.95347129, 0.30072849, -0.02144788)274.98731, 58.87479, 179.98159
13generate(-0.42445378, -0.56164614, 0.71019915), (-0.06543857, 0.80133635, 0.59462875), (-0.90308415, 0.20591935, -0.37688257)145.1562, -33.23438, 221.75583
14generate(-0.41839218, 0.55380752, 0.71988846), (0.10166334, 0.81617439, -0.5687957), (-0.90256085, -0.16478598, -0.3977822)22.49347, 67.99454, 264.08397
15generate(-0.26572512, 0.90680356, -0.32723655), (0.14798852, -0.29704467, -0.94333337), (-0.95262456, -0.29908531, -0.05526419)76.51484, 222.66664, 248.46996
16generate(-0.9999553, 0.00945898, 0.00012884), (0.00944972, 0.9995843, 0.02723674), (0.00012872, 0.02723706, -0.999629)221.2989, -3.84789, 205.71331
17generate(-0.98472807, 0.14269297, -0.09975034), (0.14268992, 0.33322118, -0.93199594), (-0.09974665, -0.93198131, -0.34849311)215.57945, 153.71638, 252.89697
18generate(-0.96264667, 0.08778264, -0.25613615), (0.08778374, -0.79370276, -0.60194338), (-0.25613525, -0.60193375, 0.75634943)235.40043, 247.59774, 119.18573
19generate(-0.96422683, -0.07938781, -0.25290871), (-0.07939036, -0.82381694, 0.56127299), (-0.25291336, 0.56126522, 0.78804377)253.36992, 148.05535, -10.63603
20generate(-0.98728482, -0.12779449, -0.09452823), (-0.12780344, 0.2844954, 0.95012769), (-0.09453352, 0.95011417, -0.29721058)244.6547, -7.3466, 42.84096
21generate(0.48539772, -0.63549143, -0.60044436), (-0.77515334, 0.00485164, -0.63176788), (0.40439449, 0.77208162, -0.49024936)188.79452, 260.03629, 26.8286
22generate(0.33348418, -0.82904072, 0.4488525), (-0.82905234, -0.4845697, -0.27906009), (0.44885601, -0.27905837, -0.84891448)117.16977, 282.30037, 173.31857
23generate(0.26698514, 0.11946381, 0.9562649), (-0.90962599, -0.29649386, 0.29100986), (0.31829742, -0.94752622, 0.02950872)-31.26211, 211.36731, 168.65994
24generate(0.37780001, 0.89922116, 0.22056615), (-0.90552425, 0.30916473, 0.29062469), (0.19314624, -0.30952208, 0.93106923)-51.37331, 145.26419, 19.29079
25generate(0.51278641, 0.43263316, -0.74153309), (-0.82241557, 0.4954065, -0.27968332), (0.24635716, 0.753254, 0.60984107)84.62917, 175.34326, -68.3658
26generate(-0.49265608, 0.63560839, 0.59437848), (-0.75922985, 0.01987339, -0.65053208), (-0.42529488, -0.77174483, 0.47278269)34.97596, 258.59508, 186.00159
27generate(-0.34125343, 0.82438417, -0.45158144), (-0.81333099, -0.49980311, -0.29782422), (-0.47122751, 0.26564987, 0.84105653)106.82698, 284.16299, 40.16316
28generate(-0.27553633, -0.12238508, -0.9534657), (-0.89805554, -0.32104923, 0.30072905), (-0.34292051, 0.93911444, -0.02144843)254.58067, 211.72989, 42.86894
29generate(-0.38632358, -0.89629646, -0.21768732), (-0.89631704, 0.30910322, 0.31794745), (-0.21768978, 0.31794373, -0.92277965)274.04645, 141.39587, 190.37964
30generate(-0.52051096, -0.42783073, 0.73893299), (-0.81051804, 0.519805, -0.26996425), (-0.26859994, -0.73942544, -0.61732802)138.32328, 170.36015, 278.84048
31generate(0.49871688, 0.64687327, -0.57690954), (0.75929997, -0.00503499, 0.65073419), (0.41804396, -0.76256966, -0.49368189)45.77752, -43.32122, 192.11157
32generate(0.51653992, -0.41245001, -0.75037863), (0.81535907, 0.50456921, 0.28391746), (0.26152112, -0.75847294, 0.59692485)176.78937, -66.54199, 95.25224
33generate(0.37780854, -0.90550725, 0.19314459), (0.89923884, 0.30915645, -0.30952601), (0.22056574, 0.29061863, 0.931069)147.22114, 7.25852, -48.84634
34generate(0.27424478, -0.15091011, 0.94974309), (0.89502028, -0.32121948, -0.30947752), (0.35177678, 0.93489618, 0.0469747)-2.06488, 76.09051, -41.04482
35generate(0.34897025, 0.80851381, 0.47382347), (0.8085333, -0.51540047, 0.28399593), (0.47382502, 0.28399002, -0.83356978)-64.76048, 44.83051, 107.87536
36generate(-0.49145853, -0.64699023, 0.58297542), (0.77508322, -0.01969004, 0.63156576), (-0.39714357, 0.76223287, 0.51114857)175.1384, -41.48602, 12.49896
37generate(-0.50877067, 0.41710656, 0.75310756), (0.82702426, 0.47980359, 0.29296685), (-0.23914962, 0.77188144, -0.5890669)43.90029, -66.09725, 108.70676
38generate(-0.36925735, 0.90842852, -0.1959438), (0.9084427, 0.30838664, -0.2822129), (-0.19594266, -0.28220685, -0.93912929)74.14671, 3.4684, 254.75818
39generate(-0.26572121, 0.14798541, -0.95262192), (0.90682101, -0.29704848, -0.29909462), (-0.32723325, -0.94331783, -0.05526428)224.07814, 71.07356, 248.81512
40generate(-0.3412457, -0.81331624, -0.47122337), (0.82440031, -0.49981102, 0.26565165), (-0.45158224, -0.29781858, 0.84105673)286.49444, 43.29019, 99.09069
41generate(0.48539786, -0.77514132, 0.40439621), (-0.63550188, 0.00485047, 0.77209514), (-0.60044362, -0.6317559, -0.49024833)99.07503, 98.00374, 290.7926
42generate(0.41921505, 0.07308444, 0.90493819), (-0.54609645, 0.81658284, 0.18703349), (-0.72528828, -0.57257868, 0.38223609)-37.79917, 61.08426, 207.20102
43generate(0.51653361, 0.81534354, 0.26151619), (-0.41245769, 0.50457537, -0.75848272), (-0.7503833, 0.28391717, 0.596925)-61.97307, 178.74076, 94.69376
44generate(0.64286259, 0.42585916, -0.63668246), (-0.41926981, -0.49998822, -0.75778222), (-0.6410482, 0.75408349, -0.14287438)59.96084, 288.37595, 108.75203
45generate(0.62361963, -0.55711455, -0.54837775), (-0.5571187, -0.80883519, 0.18816692), (-0.54838039, 0.18816642, -0.81478445)159.49404, 238.47773, 229.94777
46generate(0.49871584, 0.75928333, 0.41803782), (0.64688814, -0.00503395, -0.76257953), (-0.57691427, 0.65072782, -0.49368189)-70.24679, 116.66934, 149.44204
47generate(0.63416714, 0.55826682, -0.53493952), (0.55828415, -0.80927806, -0.18275258), (-0.53493993, -0.18274705, -0.82488908)35.94921, 153.23387, 269.7359
48generate(0.64286658, -0.41926738, -0.64104222), (0.42587202, -0.49999275, 0.75409158), (-0.63668099, -0.75776832, -0.14287383)152.07445, 36.64125, 272.23591
49generate(0.51279181, -0.82240023, 0.24636003), (0.43264081, 0.49540021, 0.75326616), (-0.74153477, -0.27967615, 0.60984196)117.6478, -71.98147, 153.48713
50generate(0.42370176, -0.09401585, 0.90090749), (0.56923628, 0.80130157, -0.18408813), (-0.70459689, 0.59082234, 0.39303066)-19.75428, -22.52139, 77.59635
51generate(-0.49146472, 0.77507116, -0.39713807), (-0.64700495, -0.01968339, 0.76224285), (0.58297413, 0.63155385, 0.5111481)123.19278, 102.97159, -82.28932
52generate(-0.42445528, -0.0654309, -0.90307935), (-0.56166246, 0.80133883, 0.20591802), (0.71019909, 0.59461697, -0.37688356)259.70087, 62.49727, 0.24805
53generate(-0.52050863, -0.81049775, -0.26860206), (-0.42784312, 0.51980337, -0.73943787), (0.73893726, -0.26996374, -0.61732872)284.9721, 176.81209, 115.91507
54generate(-0.64688231, -0.43047234, 0.62946775), (-0.43048071, -0.47521734, -0.76737511), (0.62947344, -0.76736712, 0.12209966)164.0825, 287.93685, 104.86386
55generate(-0.62893218, 0.54946314, 0.55002813), (-0.56593017, -0.80863849, 0.16071462), (0.53308293, -0.21019862, 0.81953669)64.09737, 242.30091, -17.63319
56generate(-0.49264897, -0.75921316, -0.42529596), (0.63561869, 0.01986686, -0.77175846), (0.59438376, -0.65052578, 0.47278211)292.66538, 116.17945, 59.4954
57generate(-0.62892691, -0.56592036, 0.53308067), (0.54947476, -0.80864361, -0.21019893), (0.55002912, 0.16070875, 0.81953654)186.83549, 157.00872, -59.74425
58generate(-0.63889156, 0.41442158, 0.64812809), (0.41442878, -0.52438599, 0.74382901), (0.64812703, 0.74381488, 0.16327755)69.61291, 41.63001, -65.40402
59generate(-0.50877209, 0.82701341, -0.23914532), (0.41710971, 0.47980535, 0.77189117), (0.75310953, 0.29295978, -0.58906724)102.99526, -70.50721, 50.3377
60generate(-0.4183892, 0.10166726, -0.90255787), (0.55381259, 0.81617211, -0.16479341), (0.71989435, -0.56879015, -0.39778291)240.84927, -24.43312, 127.52979

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Components

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MENGO VIRUS COAT PROTEIN (SUBUNIT ... , 4 types, 4 molecules 1234

#1: Protein MENGO VIRUS COAT PROTEIN (SUBUNIT VP1)


Mass: 30561.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengo virus / Genus: Cardiovirus / Species: Encephalomyocarditis virus / References: UniProt: P12296
#2: Protein MENGO VIRUS COAT PROTEIN (SUBUNIT VP2)


Mass: 28791.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengo virus / Genus: Cardiovirus / Species: Encephalomyocarditis virus / References: UniProt: P12296
#3: Protein MENGO VIRUS COAT PROTEIN (SUBUNIT VP3)


Mass: 25154.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengo virus / Genus: Cardiovirus / Species: Encephalomyocarditis virus / References: UniProt: P12296
#4: Protein MENGO VIRUS COAT PROTEIN (SUBUNIT VP4)


Mass: 7336.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengo virus / Genus: Cardiovirus / Species: Encephalomyocarditis virus / References: UniProt: P12296

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Non-polymers , 2 types, 234 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop / Details: took from Luo et al., 1987 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4 %PEG80001drop
25 mg/mlvirus1drop
32.8 %PEG80001reservoir
40.1 Mphosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Rmerge(I) obs: 0.112

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3→10 Å / Rfactor obs: 0.221
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 0 5 233 6507
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.03
X-RAY DIFFRACTIONp_angle_d0.0610.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0630.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.671
X-RAY DIFFRACTIONp_mcangle_it2.161.5
X-RAY DIFFRACTIONp_scbond_it0.931
X-RAY DIFFRACTIONp_scangle_it1.751.5
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1160.15
X-RAY DIFFRACTIONp_singtor_nbd0.230.5
X-RAY DIFFRACTIONp_multtor_nbd0.160.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.190.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 33000 / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

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