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- PDB-5fmo: Crystal structure and proteomics analysis of empty virus like par... -

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Entry
Database: PDB / ID: 5fmo
TitleCrystal structure and proteomics analysis of empty virus like particles of Cowpea mosaic virus
Components(EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS) x 2
KeywordsVIRUS / CPMV / EVLPS
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / : / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / GTP binding / host cell nucleus / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA2 polyprotein / RNA2 polyprotein
Similarity search - Component
Biological speciesCOWPEA MOSAIC VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuynh, N. / Hesketh, E.L. / Saxena, P. / Meshcheriakova, Y. / Ku, Y.C. / Hoang, L. / Johnson, J.E. / Ranson, N.A. / Lomonossoff, G.P. / Reddy, V.S.
CitationJournal: Structure / Year: 2016
Title: Crystal Structure and Proteomics Analysis of Empty Virus-Like Particles of Cowpea Mosaic Virus.
Authors: Huynh, N.T. / Hesketh, E.L. / Saxena, P. / Meshcheriakova, Y. / Ku, Y. / Hoang, L.T. / Johnson, J.E. / Ranson, N.A. / Lomonossoff, G.P. / Reddy, V.S.
History
DepositionNov 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Aug 23, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
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_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
S: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS


Theoretical massNumber of molelcules
Total (without water)65,0272
Polymers65,0272
Non-polymers00
Water1,04558
1
L: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
S: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
x 60


Theoretical massNumber of molelcules
Total (without water)3,901,605120
Polymers3,901,605120
Non-polymers00
Water2,162120
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
L: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
S: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
x 5


  • icosahedral pentamer
  • 325 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)325,13410
Polymers325,13410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
L: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
S: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
x 6


  • icosahedral 23 hexamer
  • 390 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)390,16112
Polymers390,16112
Non-polymers00
Water21612
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
L: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
S: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
x 60
L: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
S: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS
x 60


  • crystal asymmetric unit, crystal frame
  • 7.8 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)7,803,210240
Polymers7,803,210240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
point symmetry operation118
transform to crystal frame1
Unit cell
Length a, b, c (Å)655.970, 655.970, 571.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.61701, -0.67011, 0.412614), (-0.670113, -0.722296, -0.170993), (0.41261, -0.170991, -0.894714)63.30973, 110.77243, -68.2061
3generate(-0.252124, 0.787612, 0.562217), (-0.794834, -0.49995, 0.343935), (0.551974, -0.360166, 0.752074)206.98108, 131.38931, -91.24346
4generate(0.098683, 0.159648, -0.982224), (-0.963923, -0.229883, -0.134208), (-0.247229, 0.960036, 0.1312)148.99135, 159.34034, 40.868
5generate(-0.806289, 0.491214, -0.329555), (-0.555044, -0.435657, 0.70861), (0.204511, 0.754261, 0.623912)298.58686, 91.751, -33.80653
6generate(-0.016772, -0.835221, -0.549649), (-0.945661, 0.19179, -0.262581), (0.324727, 0.515388, -0.793053)168.07642, 156.32148, -53.67871
7generate(-0.298004, -0.326235, 0.897082), (-0.326234, -0.848391, -0.416895), (0.897092, -0.416901, 0.146395)214.56524, 53.92783, -148.29285
8generate(0.553893, -0.112186, 0.824993), (0.457134, -0.787188, -0.413955), (0.695872, 0.606422, -0.384739)73.74327, -75.56614, -115.03037
9generate(-0.118897, 0.988694, -0.09134), (-0.042908, 0.086785, 0.995299), (0.991985, 0.122256, 0.032113)184.95821, 7.0929, -163.97907
10generate(0.611626, -0.250773, -0.750343), (-0.429463, 0.691294, -0.581101), (0.664437, 0.677669, 0.315114)64.19977, 70.99189, -109.83409
11generate(-0.471588, 0.189977, -0.861109), (-0.558026, 0.69183, 0.458228), (0.682801, 0.696625, -0.220242)243.25932, 92.24401, -112.86966
12generate(0.235823, -0.967992, 0.085875), (-0.100422, -0.112162, -0.988599), (0.966598, 0.224516, -0.123661)126.32154, 16.60017, -159.78249
13generate(-0.524954, 0.323211, 0.787366), (0.323218, -0.78009, 0.535718), (0.78738, 0.535716, 0.305044)252.08099, -53.42919, -130.15702
14generate(-0.118895, -0.042916, 0.991973), (0.988699, 0.08679, 0.122258), (-0.091335, 0.995305, 0.032105)184.95777, -163.43597, 15.09805
15generate(-0.558018, 0.651396, -0.5141), (0.597799, 0.745237, 0.295398), (0.575556, -0.142486, -0.805253)257.54656, -98.81853, -95.14171
16generate(0.322548, -0.82034, -0.472222), (0.708506, 0.540069, -0.454254), (0.627687, -0.188052, 0.755417)111.98545, -117.11889, -103.75921
17generate(-0.451376, -0.496073, -0.74173), (-0.013487, 0.834929, -0.550195), (0.892239, -0.238334, -0.383553)239.91822, 2.2294, -147.49062
18generate(-0.252125, -0.794834, 0.551968), (0.787617, -0.499945, -0.360155), (0.562231, 0.343935, 0.75207)206.98134, -130.19631, -92.93911
19generate(-0.923074, 0.318439, 0.215701), (0.318446, 0.318226, 0.892927), (0.215708, 0.892935, -0.395152)317.89186, -52.64038, -35.65735
20generate(-0.471583, -0.558029, 0.682794), (0.189977, 0.69183, 0.696616), (-0.861117, 0.458236, -0.220247)243.25857, -31.40394, 142.34611
21generate(-0.962635, 0.241852, -0.121823), (0.241851, 0.565448, -0.788528), (-0.121822, -0.788528, -0.602812)324.4315, -39.97899, 20.13773
22generate(-0.369055, -0.761931, -0.532214), (0.877349, -0.47457, 0.071034), (-0.306692, -0.440729, 0.843625)226.31019, -145.02931, 50.69737
23generate(-0.773586, -0.618837, -0.136395), (0.32604, -0.204118, -0.923052), (0.543389, -0.758535, 0.35967)293.18085, -53.8957, -89.82441
24generate(-0.806289, -0.555045, 0.204506), (0.491217, -0.435656, 0.754263), (-0.329551, 0.708611, 0.62391)298.58673, -81.20021, 54.47615
25generate(-0.942176, -0.333956, -0.027891), (-0.333955, 0.928722, 0.161082), (-0.027893, 0.161093, -0.986546)321.04947, 55.20416, 4.61083
26generate(-0.016769, -0.945656, 0.32473), (-0.835226, 0.191787, 0.515377), (-0.549662, -0.262575, -0.793052)168.07595, 138.06617, 90.86131
27generate(-0.773583, 0.326038, 0.543378), (-0.618843, -0.20412, -0.75853), (-0.136397, -0.923062, 0.359669)293.18031, 102.29728, 22.54698
28generate(-0.507411, -0.156265, -0.847413), (-0.156269, -0.950427, 0.268834), (-0.84742, 0.268828, 0.457838)249.1811, 25.83189, 140.0819
29generate(-0.992935, -0.008661, 0.118342), (-0.008661, -0.989383, -0.145067), (0.11835, -0.145078, 0.982318)329.44006, 1.43169, -19.56378
30generate(-0.660832, -0.580005, -0.476331), (-0.580007, -0.00814, 0.814567), (-0.476337, 0.814575, -0.331028)274.54216, 95.87752, 78.74041
31generate(-0.555861, -0.732386, 0.393225), (-0.73239, 0.207713, -0.648433), (0.393225, -0.64843, -0.651852)257.1901, 121.06693, -65.00173
32generate(0.310058, 0.83425, -0.455947), (-0.858633, 0.451627, 0.24245), (0.408185, 0.316315, 0.856348)114.05011, 141.93548, -67.47464
33generate(0.939322, -0.213273, -0.268674), (-0.338362, -0.447141, -0.827992), (0.056448, 0.868666, -0.49218)10.03037, 55.93266, -9.33109
34generate(0.553893, 0.457131, 0.695864), (-0.112182, -0.787193, 0.606419), (0.824998, -0.41396, -0.384734)73.74326, 18.5441, -136.37547
35generate(0.935111, 0.342617, -0.090451), (0.342616, -0.939339, -0.016015), (-0.090457, -0.016016, -0.995772)10.72647, -56.63585, 14.95295
36generate(0.829602, 0.526466, 0.185991), (-0.394706, 0.31735, 0.862257), (0.394926, -0.788749, 0.471082)28.16741, 65.24654, -65.28279
37generate(0.757337, 0.638755, -0.135759), (-0.431212, 0.333041, -0.838535), (-0.490413, 0.693596, 0.527655)40.11308, 71.28106, 81.06727
38generate(-0.369052, 0.877346, -0.306696), (-0.761939, -0.474569, -0.440722), (-0.53222, 0.071025, 0.843621)226.3098, 125.95155, 87.97807
39generate(0.487589, -0.565062, -0.665543), (-0.565069, -0.785358, 0.25281), (-0.665557, 0.252813, -0.702232)84.70351, 93.40818, 110.01929
40generate(0.235827, -0.100423, 0.966588), (-0.967996, -0.112169, 0.224511), (0.085869, -0.988605, -0.123658)126.3209, 160.01366, -14.1945
41generate(0.939323, -0.338357, 0.056453), (-0.213274, -0.447149, 0.86866), (-0.268684, -0.827996, -0.492173)10.03021, 35.25502, 44.41449
42generate(0.322554, 0.708501, 0.627675), (-0.820347, 0.540066, -0.188053), (-0.47223, -0.454261, 0.755414)111.98459, 135.60665, 78.06152
43generate(0.364699, 0.602324, -0.710068), (-0.058956, -0.746126, -0.663183), (-0.929264, 0.283721, -0.236607)105.01778, 9.74561, 153.61106
44generate(-0.693936, 0.351671, -0.628315), (0.351668, -0.59593, -0.721934), (-0.628318, -0.721945, 0.289866)280.0144, -58.13205, 103.86345
45generate(0.098684, -0.963916, -0.247223), (0.159647, -0.229887, 0.960032), (-0.982234, -0.134209, 0.131203)148.99112, -26.39035, 162.36728
46generate(-0.45137, -0.01349, 0.892228), (-0.496078, 0.834927, -0.238341), (-0.741741, -0.550194, -0.383557)239.91722, 82.00374, 122.6128
47generate(0.611631, -0.429462, 0.664432), (-0.250775, 0.691288, 0.677661), (-0.750354, -0.581102, 0.315116)64.19901, 41.45418, 124.03658
48generate(-0.21561, 0.943214, 0.252688), (-0.016317, 0.255264, -0.966732), (-0.976348, -0.212564, -0.039655)200.94513, 2.69728, 161.39428
49generate(0.364698, -0.058948, -0.929251), (0.602323, -0.74613, 0.283725), (-0.710076, -0.663191, -0.236601)105.01801, -99.56644, 117.37832
50generate(-0.215615, -0.016309, -0.976337), (0.94322, 0.255262, -0.21256), (0.252695, -0.966736, -0.039647)200.94598, -155.91803, -41.77156
51generate(0.31006, -0.858631, 0.408182), (0.834254, 0.451629, 0.316318), (-0.455946, 0.242452, 0.856346)114.0499, -137.90544, 75.36974
52generate(-0.558014, 0.597791, 0.575547), (0.651397, 0.745239, -0.142491), (-0.514104, 0.295405, -0.805259)257.54596, -107.6786, 84.98338
53generate(0.404894, 0.195206, 0.893279), (0.281937, 0.902691, -0.325057), (-0.869817, 0.383466, 0.310449)98.37343, -46.60539, 143.78419
54generate(-0.041164, 0.90624, -0.420751), (0.906242, -0.143469, -0.397672), (-0.420755, -0.397675, -0.815367)172.1086, -149.80535, 69.55244
55generate(0.757335, -0.431204, -0.490405), (0.63876, 0.333035, 0.693595), (-0.135759, -0.83854, 0.527664)40.11345, -105.58956, 22.44146
56generate(0.404888, 0.281941, -0.869808), (0.195213, 0.902688, 0.383462), (0.893289, -0.325056, 0.310458)98.37441, -32.2695, -147.66433
57generate(0.829602, -0.394709, 0.394925), (0.526467, 0.317358, -0.788742), (0.185995, 0.862263, 0.471073)28.16744, -87.02702, -30.74569
58generate(0.063273, 0.888651, 0.454188), (0.888659, -0.257286, 0.379599), (0.454195, 0.379602, -0.805986)154.8448, -146.89882, -75.08017
59generate(0.604815, 0.672377, 0.426735), (0.648674, -0.105091, -0.753772), (-0.461978, 0.732709, -0.499724)65.32558, -107.22836, 76.3668
60generate(0.604812, 0.648676, -0.461973), (0.672384, -0.105099, 0.732705), (0.426739, -0.753777, -0.499714)65.32609, -111.14778, -70.5417
61generate(-0.178912, 0.874231, -0.45135), (0.794478, 0.398973, 0.457851), (0.580347, -0.276674, -0.765928)357.55984, 32.00665, 48.64338
62generate(-0.882456, -0.434386, 0.18052), (0.411757, -0.898853, -0.150055), (0.227453, -0.058089, 0.972055)473.85848, 95.27185, 106.97807
63generate(-0.898894, -0.415424, -0.139357), (-0.264703, 0.261371, 0.928228), (-0.349181, 0.871272, -0.344911)476.57581, 207.09346, 202.29805
64generate(-0.74876, -0.662846, -0.000815), (-0.419372, 0.474673, -0.77383), (0.513322, -0.579064, -0.633388)451.75797, 232.66093, 59.72276
65generate(-0.433288, -0.809184, 0.396848), (-0.768391, 0.561782, 0.306551), (-0.471002, -0.1721, -0.865182)399.60925, 290.35512, 222.43551
66generate(-0.970291, 0.084479, 0.226727), (-0.241941, -0.351074, -0.904546), (0.003189, -0.932531, 0.361083)488.37793, 203.33088, 144.0499
67generate(-0.63679, -0.495154, -0.591037), (0.043818, -0.78855, 0.613408), (-0.769792, 0.364714, 0.523835)433.24895, 156.09376, 271.82676
68generate(-0.013539, -0.941821, -0.335841), (0.941045, -0.125545, 0.314128), (-0.338015, -0.311788, 0.887994)330.22303, 7.77845, 200.45216
69generate(-0.463972, -0.156199, 0.871969), (0.3426, 0.876095, 0.339233), (-0.816919, 0.456135, -0.352978)404.68145, 106.7038, 279.61694
70generate(-0.78477, 0.343351, -0.515998), (0.618792, 0.386845, -0.683699), (-0.035134, -0.855843, -0.516038)457.71068, 61.0482, 150.38486
71generate(-0.711654, 0.256408, 0.654066), (-0.284683, 0.745904, -0.60215), (-0.642269, -0.614723, -0.457832)445.62417, 210.39622, 250.74659
72generate(-0.566258, -0.026206, -0.823814), (0.589848, -0.711003, -0.382817), (-0.575701, -0.702702, 0.418072)421.58966, 65.83282, 239.74265
73generate(0.021103, -0.9816, 0.18979), (0.072393, 0.190826, 0.978946), (-0.997157, -0.006915, 0.075084)324.49652, 151.37011, 309.41106
74generate(0.926847, -0.365678, -0.085085), (0.258188, 0.456232, 0.851577), (-0.272591, -0.811251, 0.517273)174.77344, 120.65756, 189.63746
75generate(0.362673, 0.599278, 0.713676), (0.058692, 0.749612, -0.659271), (-0.930073, 0.280982, 0.23668)268.03374, 153.63503, 298.32184
76generate(0.278383, 0.70379, -0.653595), (0.82632, -0.522368, -0.210537), (-0.489598, -0.481471, -0.726966)281.96712, 26.74308, 225.50955
77generate(-0.333746, 0.926246, -0.175177), (0.044523, -0.170126, -0.984411), (-0.941613, -0.33635, 0.015538)383.15457, 155.97714, 300.22943
78generate(0.479904, -0.450097, -0.75306), (0.371348, -0.673472, 0.63917), (-0.794862, -0.586386, -0.156053)248.65489, 101.95166, 275.97086
79generate(0.346184, -0.181796, 0.920385), (-0.507549, 0.788787, 0.346703), (-0.789025, -0.587164, 0.18079)270.75934, 247.23683, 275.00602
80generate(0.639121, 0.497832, 0.586252), (-0.69313, 0.042483, 0.719556), (0.33331, -0.866237, 0.372214)222.33577, 277.91409, 89.47951
81generate(0.438645, 0.806964, -0.395481), (-0.724077, 0.056716, -0.687385), (-0.532269, 0.587869, 0.609176)255.47518, 283.02978, 232.56321
82generate(0.971459, -0.079642, -0.22345), (-0.083586, -0.996466, -0.008238), (-0.222016, 0.026684, -0.974677)167.39892, 177.15407, 181.27705
83generate(0.178179, 0.274636, -0.944895), (-0.235725, -0.920386, -0.311961), (-0.955352, 0.278317, -0.099254)298.53131, 202.30321, 302.50043
84generate(0.722435, -0.601392, 0.341209), (-0.595481, -0.290348, 0.749064), (-0.351421, -0.744329, -0.567871)208.5636, 261.77239, 202.66837
85generate(-0.110798, 0.798956, 0.59109), (-0.894548, 0.178971, -0.409582), (-0.433028, -0.574149, 0.694869)346.30037, 311.20936, 216.15824
86generate(-0.47909, 0.455368, 0.750405), (-0.598218, -0.795005, 0.100513), (0.642355, -0.400757, 0.653285)407.18049, 262.22486, 38.39319
87generate(-0.341046, 0.179844, -0.922684), (-0.923946, -0.245033, 0.293743), (-0.173258, 0.952688, 0.249733)384.36126, 316.06891, 173.21724
88generate(0.33665, -0.92427, 0.17999), (-0.853466, -0.38026, -0.356372), (0.397824, -0.033632, -0.916843)272.33544, 304.4183, 78.81518
89generate(0.116659, -0.797919, -0.591364), (-0.738133, -0.468042, 0.485897), (-0.664498, 0.379829, -0.643568)308.70086, 285.35337, 254.42114
90generate(-0.173835, -0.271005, 0.946751), (-0.974515, -0.091095, -0.205005), (0.141801, -0.958258, -0.248263)356.72058, 324.4282, 121.13674
91generate(-0.71831, 0.605291, -0.343019), (-0.553785, -0.795877, -0.244749), (-0.421141, 0.014144, 0.906883)446.72447, 254.87985, 214.19335
92generate(-0.990351, 0.102801, -0.092981), (0.090651, 0.987805, 0.126571), (0.104862, 0.116926, -0.987588)491.69399, 148.35208, 127.24282
93generate(-0.48934, -0.74482, -0.453641), (0.637117, 0.049881, -0.769147), (0.595513, -0.665395, 0.450134)408.87493, 58.01894, 46.1363
94generate(-0.569534, -0.583134, 0.579302), (0.773024, -0.14042, 0.618643), (-0.279401, 0.800154, 0.53074)422.13121, 35.55303, 190.7631
95generate(0.173051, -0.875268, 0.451624), (0.838203, -0.109902, -0.534166), (0.517179, 0.470994, 0.714627)299.37893, 24.77862, 59.08524
96generate(-0.67174, 0.539248, 0.507913), (0.68244, 0.18375, 0.707468), (0.288177, 0.821855, -0.49144)439.02629, 50.52688, 96.94012
97generate(-0.291127, -0.13618, -0.946942), (0.20511, 0.957915, -0.200823), (0.934444, -0.252688, -0.250932)376.1095, 129.43153, -9.8904
98generate(-0.359865, -0.603908, -0.71119), (-0.840874, 0.54021, -0.033247), (0.404272, 0.586066, -0.702207)387.47214, 302.33686, 77.74917
99generate(-0.280837, -0.699595, 0.65704), (-0.142794, -0.646516, -0.749412), (0.94908, -0.30428, 0.081667)374.40846, 186.94146, -12.30965
100generate(-0.927201, 0.366113, 0.079153), (-0.15953, -0.577169, 0.80089), (0.338911, 0.729954, 0.593553)481.2551, 189.70801, 88.55364
101generate(-0.233236, 0.04334, 0.971451), (0.538163, -0.826316, 0.166081), (0.809932, 0.561535, 0.169396)366.53985, 74.37643, 10.69194
102generate(-0.56174, 0.550414, -0.617657), (-0.287246, 0.570376, 0.769513), (0.775856, 0.609685, -0.162294)420.8429, 210.81985, 16.32496
103generate(0.302634, -0.888107, -0.345944), (-0.15924, 0.31075, -0.937056), (0.939712, 0.33868, -0.047376)277.95845, 189.66009, -10.76122
104generate(0.715183, -0.258049, -0.649555), (-0.698687, -0.288908, -0.654499), (-0.018775, 0.921927, -0.386917)209.76234, 278.83267, 147.68053
105generate(0.565245, 0.032056, 0.824302), (-0.307619, -0.918976, 0.246686), (0.765421, -0.393007, -0.509583)234.5478, 214.18769, 18.04981
106generate(-0.018147, 0.980662, -0.194877), (-0.896132, 0.070489, 0.438152), (0.443421, 0.182577, 0.877521)330.9847, 311.47118, 71.27771
107generate(0.010009, 0.943461, 0.33133), (0.042324, -0.331451, 0.942521), (0.999058, 0.004584, -0.043246)326.33047, 156.34066, -20.57128
108generate(0.464985, 0.150349, -0.872457), (-0.624829, 0.753884, -0.203101), (0.627198, 0.639575, 0.444489)251.12109, 266.62369, 40.89861
109generate(0.781814, -0.342413, 0.521085), (0.204947, -0.648161, -0.733399), (0.58887, 0.680181, -0.436568)198.7481, 129.45851, 47.23437
110generate(0.749114, 0.662412, 0.006747), (0.320715, -0.353736, -0.878636), (-0.579642, 0.660361, -0.477438)204.15349, 110.32151, 240.39415
111generate(0.879648, 0.439016, -0.183006), (0.370425, -0.390969, 0.842572), (0.298348, -0.808959, -0.506528)182.57563, 102.10426, 95.25893
112generate(0.901348, 0.411228, 0.135911), (-0.418822, 0.907513, 0.031721), (-0.1103, -0.085521, 0.990211)178.98861, 232.57, 162.81005
113generate(0.56663, 0.581158, -0.584114), (0.035919, 0.690807, 0.72214), (0.823191, -0.430171, 0.370565)234.31878, 157.39952, 8.50028
114generate(0.989537, -0.108072, 0.095636), (0.136219, 0.480672, -0.866254), (0.047645, 0.870218, 0.490356)164.41063, 140.8194, 136.70112
115generate(0.484202, 0.746772, 0.45594), (0.794377, -0.593636, 0.128701), (0.36677, 0.299871, -0.880657)247.94446, 32.02332, 83.94843
116generate(-0.304964, 0.885429, 0.350728), (0.808552, 0.435317, -0.395908), (-0.50323, 0.162843, -0.848673)378.39683, 29.68007, 227.76295
117generate(0.227879, -0.04112, -0.972818), (0.954304, 0.207818, 0.214753), (0.193339, -0.977304, 0.08661)290.31572, 5.58666, 112.61734
118generate(0.560572, -0.555251, 0.61438), (0.612773, 0.777164, 0.143271), (-0.557029, 0.296162, 0.775888)235.32025, 62.0432, 236.65609
119generate(0.667396, -0.542879, -0.509768), (0.527799, 0.827731, -0.190502), (0.525373, -0.141915, 0.838956)217.66182, 76.08971, 57.73072
120generate(0.287002, 0.132281, 0.948752), (0.944156, 0.12831, -0.303492), (-0.161882, 0.982873, -0.08808)280.54243, 7.26423, 171.33668

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Components

#1: Protein EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS


Mass: 41298.930 Da / Num. of mol.: 1 / Fragment: LARGE SUBUNIT
Source method: isolated from a genetically manipulated source
Details: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS / Source: (gene. exp.) COWPEA MOSAIC VIRUS / Plasmid: CPMV-HT, PEAQ VECTOR / Production host: VIGNA UNGUICULATA (cowpea) / References: UniProt: Q66170, UniProt: P03599*PLUS
#2: Protein EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS


Mass: 23727.824 Da / Num. of mol.: 1 / Fragment: SMALL SUBUNIT
Source method: isolated from a genetically manipulated source
Details: EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS / Source: (gene. exp.) COWPEA MOSAIC VIRUS / Plasmid: CPMV-HT, PEAQ VECTOR / Production host: VIGNA UNGUICULATA (cowpea) / References: UniProt: Q66170, UniProt: P03599*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.85 %
Description: DATA WAS COLLECTED USING THE OSCILLATION METHOD
Crystal growpH: 4.8
Details: 0.1M SODIUM ACETATE PH 4.7 3-4%(W/V)PEG 3350 0.3M AMMONIUM SULFATE 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.85506
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 3, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85506 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 3192363 / % possible obs: 60.3 % / Observed criterion σ(I): 1.7 / Redundancy: 2.3 % / Biso Wilson estimate: 1.48 Å2 / Rmerge(I) obs: 0.29 / Net I/σ(I): 3.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 49.6

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
HKL-2000data reduction
SCALEPACKdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NY7

1ny7


Resolution: 2.3→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 3
Details: STRICT NCS CONSTRAINTS WERE EMPLOYED. GLY L 370 TO GLN L 374, PHE S 568 TO ALA S 587
RfactorNum. reflection% reflectionSelection details
Rfree0.362 95172 3 %RANDOM
Rwork0.359 ---
obs0.359 3192363 58.3 %-
Displacement parametersBiso mean: 24.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 0 58 4440
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.566
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.378
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.77
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTAINTS
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4449 --
Rwork0.4402 122351 -
obs--49.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO

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