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- PDB-3r0r: The 2.3 A structure of porcine circovirus 2 -

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Basic information

Entry
Database: PDB / ID: 3r0r
TitleThe 2.3 A structure of porcine circovirus 2
ComponentsPorcine circovirus 2 (PCV2) capsid protein
KeywordsVIRUS / Viral jelly roll / beta barrel / ssDNA
Function / homology
Function and homology information


viral capsid assembly / T=1 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Circovirus capsid protein / Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPorcine circovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKhayat, R. / Speir, J.A. / Johnson, J.E.
CitationJournal: J.Virol. / Year: 2011
Title: The 2.3-angstrom structure of porcine circovirus 2.
Authors: Khayat, R. / Brunn, N. / Speir, J.A. / Hardham, J.M. / Ankenbauer, R.G. / Schneemann, A. / Johnson, J.E.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3May 30, 2012Group: Refinement description
Revision 1.4Oct 29, 2014Group: Structure summary
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / 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_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _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
A: Porcine circovirus 2 (PCV2) capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5195
Polymers26,1351
Non-polymers3844
Water2,306128
1
A: Porcine circovirus 2 (PCV2) capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,591,168300
Polymers1,568,11360
Non-polymers23,055240
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2
A: Porcine circovirus 2 (PCV2) capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,591,168300
Polymers1,568,11360
Non-polymers23,055240
Water1,08160
TypeNameSymmetry operationNumber
point symmetry operation60
3


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Porcine circovirus 2 (PCV2) capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 133 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)132,59725
Polymers130,6765
Non-polymers1,92120
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
5
A: Porcine circovirus 2 (PCV2) capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 159 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)159,11730
Polymers156,8116
Non-polymers2,30624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
6


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
7
A: Porcine circovirus 2 (PCV2) capsid protein
hetero molecules
x 120


  • crystal asymmetric unit, crystal frame
  • 3.18 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)3,182,337600
Polymers3,136,226120
Non-polymers46,110480
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation119
Unit cell
Length a, b, c (Å)193.612, 202.163, 230.975
Angle α, β, γ (deg.)90.010, 89.330, 90.070
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.318191, -0.741846, 0.590271), (0.829661, 0.519168, 0.205249), (-0.458713, 0.424416, 0.780675)
3generate(-0.785, -0.370663, 0.49637), (0.600574, -0.258827, 0.756518), (-0.151939, 0.891974, 0.42579)
4generate(-0.784999, 0.600576, -0.151939), (-0.370665, -0.258828, 0.891973), (0.496371, 0.756516, 0.425792)
5generate(0.318185, 0.829663, -0.458713), (-0.741849, 0.519163, 0.424416), (0.590269, 0.205253, 0.780675)
6generate(-0.955802, 0.009108, 0.293871), (0.009122, -0.99812, 0.060604), (0.29387, 0.060606, 0.953922)
7generate(-0.137426, -0.727944, 0.671723), (0.779122, -0.498192, -0.380491), (0.611624, 0.471065, 0.635622)
8generate(0.322101, 0.76604, 0.556267), (-0.861051, 0.481281, -0.164193), (-0.393499, -0.426088, 0.814621)
9generate(-0.137423, 0.779124, 0.611621), (-0.727944, -0.498189, 0.471068), (0.671723, -0.38049, 0.635622)
10generate(-0.260688, 0.416013, 0.871192), (0.41602, -0.765904, 0.490222), (0.871188, 0.490228, 0.026592)
11generate(0.508974, -0.364811, 0.779652), (-0.260548, 0.797968, 0.543472), (-0.820402, -0.47975, 0.311094)
12generate(0.892792, 0.392898, 0.220347), (-0.354072, 0.30966, 0.882465), (0.278486, -0.865876, 0.415576)
13generate(0.711125, -0.615811, -0.339231), (0.61405, 0.309019, 0.726258), (-0.342409, -0.724765, 0.59789)
14generate(0.482866, 0.200649, -0.852397), (0.394835, 0.818951, 0.416442), (0.78163, -0.537642, 0.31622)
15generate(-0.710195, -0.247534, -0.659052), (-0.247534, -0.788571, 0.562923), (-0.659052, 0.562923, 0.498766)
16generate(-0.431357, -0.853008, -0.293783), (0.83852, -0.499221, 0.218318), (-0.332889, -0.15217, 0.930607)
17generate(0.322107, -0.861049, -0.393499), (0.766037, 0.481286, -0.426088), (0.556268, -0.164189, 0.814621)
18generate(-0.431357, 0.83852, -0.332889), (-0.853008, -0.499221, -0.15217), (-0.293783, 0.218318, 0.930607)
19generate(0.508976, -0.260548, -0.820401), (-0.364807, 0.79797, -0.47975), (0.779653, 0.543469, 0.311098)
20generate(-0.729947, 0.214989, -0.648812), (0.214962, -0.828869, -0.516495), (-0.648821, -0.516484, 0.558817)
21generate(-0.774722, -0.627165, -0.080435), (0.378419, -0.357975, -0.853612), (0.506562, -0.691749, 0.514663)
22generate(0.712196, 0.612808, -0.342409), (-0.615271, 0.310094, -0.724764), (-0.337962, 0.726848, 0.597891)
23generate(0.892791, -0.354076, 0.278486), (0.3929, 0.30966, -0.865876), (0.22035, 0.882463, 0.415578)
24generate(-0.774722, 0.378419, 0.506562), (-0.627165, -0.357975, -0.691749), (-0.080435, -0.853612, 0.514663)
25generate(-0.228231, -0.342324, 0.911441), (-0.342316, -0.848163, -0.404276), (0.911444, -0.404269, 0.076394)
26generate(0.482866, 0.394835, 0.78163), (0.200649, 0.818951, -0.537642), (-0.852397, 0.416442, 0.31622)
27generate(0.122676, 0.178514, 0.97626), (0.98992, 0.048138, -0.133195), (-0.070773, 0.982759, -0.17081)
28generate(0.122676, 0.98992, -0.070773), (0.178514, 0.048138, 0.982759), (0.97626, -0.133195, -0.17081)
29generate(-0.129023, -0.991231, 0.028537), (0.11862, 0.013144, 0.992853), (-0.984521, 0.131486, 0.115884)
30generate(-0.129023, 0.118621, -0.984521), (-0.991231, 0.013137, 0.131486), (0.028531, 0.992853, 0.115885)
31generate(0.16955, -0.985168, 0.026407), (-0.117976, -0.046892, -0.991909), (0.978435, 0.165063, -0.124176)
32generate(-0.164921, 0.98618, 0.015831), (-0.179241, -0.014184, -0.983703), (-0.969883, -0.165071, 0.179103)
33generate(-0.684585, -0.625823, 0.37375), (-0.625821, 0.241707, -0.74157), (0.373754, -0.741568, -0.557122)
34generate(0.8007, -0.363802, -0.47595), (-0.588077, -0.325856, -0.740259), (0.114216, 0.87262, -0.474856)
35generate(0.243718, 0.377739, -0.893261), (-0.382351, -0.809014, -0.446434), (-0.891296, 0.450343, -0.052742)
36generate(-0.285517, -0.786395, -0.54778), (-0.850834, 0.471059, -0.232778), (0.441092, 0.399607, -0.803587)
37generate(-0.907899, 0.343153, -0.240761), (0.342047, 0.274417, -0.898721), (-0.242329, -0.898299, -0.366517)
38generate(-0.491615, -0.42759, -0.758605), (0.227733, 0.7777, -0.585936), (0.840507, -0.460815, -0.284952)
39generate(-0.498357, 0.329828, -0.801781), (-0.236084, 0.83823, 0.491563), (0.834209, 0.434262, -0.339871)
40generate(-0.164922, -0.17924, -0.969883), (0.98618, -0.014186, -0.165071), (0.015829, -0.983703, 0.179103)
41generate(-0.737094, 0.601203, 0.308622), (0.6012, 0.3748, 0.70575), (0.308627, 0.705748, -0.637706)
42generate(0.758457, 0.382439, -0.527715), (0.641057, -0.291897, 0.709818), (0.117424, -0.876662, -0.466556)
43generate(-0.352391, 0.720428, -0.597331), (0.840133, 0.524731, 0.137235), (0.412306, -0.453478, -0.790166)
44generate(0.243718, -0.382351, -0.891296), (0.377739, -0.809014, 0.450343), (-0.893261, -0.446434, -0.052742)
45generate(-0.876535, -0.40678, -0.257326), (-0.40678, 0.340217, 0.84781), (-0.257326, 0.84781, -0.463683)
46generate(-0.285408, -0.850508, 0.44179), (-0.786718, 0.471174, 0.398835), (-0.547372, -0.233734, -0.803587)
47generate(-0.353879, 0.839505, 0.412311), (0.719498, 0.526009, -0.453473), (-0.597572, 0.136182, -0.790166)
48generate(0.954887, 0.033577, -0.295064), (0.033577, -0.999423, -0.005068), (-0.295064, -0.005068, -0.955464)
49generate(0.106074, 0.748924, -0.654111), (0.748248, -0.493359, -0.443532), (-0.654884, -0.44239, -0.612714)
50generate(0.169182, -0.757594, -0.630419), (-0.757594, -0.509102, 0.408492), (-0.630419, 0.408492, -0.66008)
51generate(-0.999088, -0.04269, 0.00109), (-0.042684, 0.997544, -0.055532), (0.001284, -0.055528, -0.998456)
52generate(0.758457, 0.641057, 0.117423), (0.382439, -0.291897, -0.876662), (-0.527715, 0.709818, -0.466556)
53generate(0.465612, -0.816989, 0.340197), (-0.817127, -0.544502, -0.189265), (0.339865, -0.18986, -0.921111)
54generate(-0.492011, 0.226874, 0.840508), (-0.428948, 0.776953, -0.460813), (-0.757581, -0.587259, -0.284952)
55generate(0.171269, -0.117895, 0.978145), (-0.984871, -0.047093, 0.16677), (0.026402, -0.991909, -0.124176)
56generate(0.719329, -0.179991, 0.670946), (0.281659, -0.807327, -0.518547), (0.635007, 0.561984, -0.530038)
57generate(0.394759, 0.873366, 0.285302), (0.873366, -0.453118, 0.178648), (0.285301, 0.17865, -0.941641)
58generate(0.801087, -0.58725, 0.115746), (-0.364637, -0.325462, 0.872419), (-0.474657, -0.741089, -0.474856)
59generate(-0.498356, -0.236081, 0.834211), (0.32983, 0.838231, 0.434259), (-0.801781, 0.491563, -0.339871)
60generate(0.719014, 0.28024, 0.635991), (-0.181256, -0.807818, 0.560871), (0.670943, -0.518551, -0.530038)
61generate(0.99915, 0.041216, -0.001117), (-0.041213, 0.99755, -0.056535), (-0.001216, 0.056533, 0.9984)97.441, 101.048, 114.781
62generate(0.351957, -0.720663, 0.597303), (0.840412, 0.52426, 0.137326), (-0.412108, 0.453648, 0.790171)97.441, 101.048, 114.781
63generate(-0.75989, -0.381777, 0.52613), (0.639388, -0.292969, 0.710881), (-0.117258, 0.876593, 0.466728)97.441, 101.048, 114.781
64generate(-0.799865, 0.588821, -0.116212), (-0.365746, -0.324687, 0.872243), (0.475863, 0.740181, 0.475065)97.441, 101.048, 114.781
65generate(0.287301, 0.849738, -0.442044), (-0.785861, 0.472961, 0.398409), (0.547613, 0.232922, 0.803659)97.441, 101.048, 114.781
66generate(-0.954922, -0.031424, 0.295189), (0.03129, -0.999497, -0.005181), (0.295203, 0.004289, 0.955425)97.441, 101.048, 114.781
67generate(-0.106417, -0.748671, 0.654345), (0.748009, -0.49385, -0.443391), (0.655102, 0.442271, 0.612566)97.441, 101.048, 114.781
68generate(0.287284, 0.785641, 0.547939), (-0.849738, 0.473048, -0.232744), (-0.442055, -0.398741, 0.803488)97.441, 101.048, 114.781
69generate(-0.16878, 0.757833, 0.63024), (-0.757833, -0.508623, 0.408646), (0.63024, -0.408645, 0.660156)97.441, 101.048, 114.781
70generate(-0.243896, 0.382742, 0.89108), (0.37738, -0.808951, 0.450757), (0.893364, 0.446213, 0.052861)97.441, 101.048, 114.781
71generate(0.498462, -0.330251, 0.801542), (-0.235619, 0.838179, 0.491873), (-0.834278, -0.434038, 0.339987)97.441, 101.048, 114.781
72generate(0.876737, 0.40661, 0.256907), (-0.406409, 0.340625, 0.847825), (0.257225, -0.847728, 0.463888)97.441, 101.048, 114.781
73generate(0.73677, -0.601397, -0.309017), (0.601675, 0.374637, 0.705432), (-0.308475, -0.70567, 0.637866)97.441, 101.048, 114.781
74generate(0.498177, 0.235645, -0.83444), (0.329887, 0.83848, 0.433735), (0.801869, -0.491348, 0.339976)97.441, 101.048, 114.781
75generate(-0.718908, -0.279817, -0.636297), (-0.181471, -0.808097, 0.560399), (-0.670999, 0.518345, 0.530169)97.441, 101.048, 114.781
76generate(-0.395251, -0.873082, -0.285491), (0.873192, -0.453598, 0.178284), (-0.285154, -0.178821, 0.941653)97.441, 101.048, 114.781
77generate(0.352275, -0.840655, -0.411341), (0.720093, 0.524203, -0.454617), (0.597802, -0.136053, 0.790014)97.441, 101.048, 114.781
78generate(-0.465221, 0.817218, -0.340184), (-0.81723, -0.544195, -0.189702), (-0.340154, 0.189755, 0.921026)97.441, 101.048, 114.781
79generate(0.49295, -0.228604, -0.839488), (-0.428064, 0.776286, -0.462754), (0.75747, 0.587469, 0.284813)97.441, 101.048, 114.781
80generate(-0.719447, 0.180377, -0.670716), (0.281501, -0.807088, -0.519005), (-0.634943, -0.562205, 0.529881)97.441, 101.048, 114.781
81generate(-0.758637, -0.640919, -0.117013), (0.38193, -0.291993, -0.876852), (0.527825, -0.709903, 0.466303)97.441, 101.048, 114.781
82generate(0.685964, 0.625285, -0.372119), (-0.624203, 0.242868, -0.742554), (-0.373932, 0.741642, 0.556903)97.441, 101.048, 114.781
83generate(0.907725, -0.343297, 0.241211), (0.342434, 0.273988, -0.898704), (0.242434, 0.898375, 0.366263)97.441, 101.048, 114.781
84generate(-0.799769, 0.365354, 0.476325), (-0.589012, -0.324386, -0.740161), (-0.115907, -0.872519, 0.474632)97.441, 101.048, 114.781
85generate(-0.243515, -0.377322, 0.893492), (-0.382716, -0.809089, -0.445985), (0.891195, -0.450558, 0.052618)97.441, 101.048, 114.781
86generate(0.491486, 0.427193, 0.758912), (0.228226, 0.777791, -0.585623), (-0.840449, 0.461029, 0.284777)97.441, 101.048, 114.781
87generate(0.16442, 0.179245, 0.969968), (0.986268, -0.014366, -0.164528), (-0.015556, 0.9837, -0.179146)97.441, 101.048, 114.781
88generate(0.12897, 0.991223, -0.029034), (0.118416, 0.013675, 0.99287), (0.984553, -0.131488, -0.115613)97.441, 101.048, 114.781
89generate(-0.122763, -0.989945, 0.070275), (0.178705, 0.047603, 0.98275), (-0.976214, 0.133204, 0.171064)97.441, 101.048, 114.781
90generate(-0.170728, 0.116208, -0.978441), (-0.984957, -0.047009, 0.166282), (-0.026672, 0.992112, 0.122486)97.441, 101.048, 114.781
91generate(0.16501, -0.986173, -0.015332), (-0.179403, -0.014725, -0.983666), (0.969838, 0.165065, -0.179352)97.441, 101.048, 114.781
92generate(-0.169489, 0.985192, -0.025906), (-0.117795, -0.046349, -0.991956), (-0.978467, -0.165074, 0.123906)97.441, 101.048, 114.781
93generate(-0.710786, -0.613511, 0.344074), (-0.616982, 0.30886, -0.723836), (0.337811, -0.72678, -0.598059)97.441, 101.048, 114.781
94generate(0.775463, -0.378966, -0.505017), (-0.626077, -0.357937, -0.692755), (0.081766, 0.853385, -0.514829)97.441, 101.048, 114.781
95generate(0.228384, 0.342729, -0.91125), (-0.341959, -0.848112, -0.404686), (-0.91154, 0.404034, -0.076496)97.441, 101.048, 114.781
96generate(-0.321488, -0.766534, -0.555942), (-0.86103, 0.480961, -0.165237), (0.394046, 0.425561, -0.814632)97.441, 101.048, 114.781
97generate(-0.892991, 0.353915, -0.278048), (0.3925, 0.310056, -0.865915), (-0.22025, -0.882389, -0.415789)97.441, 101.048, 114.781
98generate(-0.4833, -0.396672, -0.780431), (0.199353, 0.818172, -0.539309), (0.852455, -0.416229, -0.316345)97.441, 101.048, 114.781
99generate(-0.508834, 0.364408, -0.779932), (-0.261028, 0.798025, 0.543158), (0.820337, 0.479962, -0.310942)97.441, 101.048, 114.781
100generate(-0.123165, -0.178532, -0.976195), (0.989841, 0.048309, -0.133722), (0.071033, -0.982747, 0.170768)97.441, 101.048, 114.781
101generate(-0.711408, 0.61566, 0.338912), (0.613626, 0.309081, 0.72659), (0.342581, 0.724867, -0.597667)97.441, 101.048, 114.781
102generate(0.784695, 0.37079, -0.496758), (0.600931, -0.258387, 0.756385), (0.152104, -0.892049, -0.425574)97.441, 101.048, 114.781
103generate(-0.318576, 0.741564, -0.590417), (0.829373, 0.519656, 0.205178), (0.458966, -0.424311, -0.780583)97.441, 101.048, 114.781
104generate(0.260467, -0.415615, -0.871448), (0.416385, -0.765993, 0.489774), (-0.87108, -0.490428, -0.02646)97.441, 101.048, 114.781
105generate(-0.892001, -0.393584, -0.222318), (-0.355986, 0.30854, 0.882087), (-0.278581, 0.865965, -0.415328)97.441, 101.048, 114.781
106generate(-0.31783, -0.829888, 0.458553), (-0.741813, 0.518854, 0.424858), (-0.590506, -0.205128, -0.780529)97.441, 101.048, 114.781
107generate(-0.322527, 0.860768, 0.393771), (0.765977, 0.481743, -0.42568), (-0.556108, 0.164326, -0.814703)97.441, 101.048, 114.781
108generate(0.955757, -0.008641, -0.29403), (0.009664, -0.998106, 0.060746), (-0.293998, -0.0609, -0.953864)97.441, 101.048, 114.781
109generate(0.137021, 0.728177, -0.671553), (0.77935, -0.497707, -0.380658), (-0.611424, -0.471217, -0.635701)97.441, 101.048, 114.781
110generate(0.139969, -0.778523, -0.611809), (-0.728154, -0.49964, 0.469203), (-0.67097, 0.379818, -0.636819)97.441, 101.048, 114.781
111generate(0.774959, 0.62662, 0.082374), (0.379678, -0.357386, -0.853299), (-0.505255, 0.692548, -0.514874)97.441, 101.048, 114.781
112generate(0.431825, -0.838106, 0.333326), (-0.852954, -0.499608, -0.151196), (0.293251, -0.219021, -0.930609)97.441, 101.048, 114.781
113generate(-0.508773, 0.260145, 0.820655), (-0.364869, 0.798245, -0.479245), (-0.779757, -0.543258, -0.311207)97.441, 101.048, 114.781
114generate(0.129514, -0.118624, 0.984456), (-0.991159, 0.013357, 0.132005), (-0.028808, -0.992849, -0.115846)97.441, 101.048, 114.781
115generate(0.72907, -0.214372, 0.650002), (0.215025, -0.829863, -0.514871), (0.649786, 0.515143, -0.558932)97.441, 101.048, 114.781
116generate(0.430985, 0.853199, 0.293776), (0.838584, -0.498923, 0.218751), (0.33321, 0.152077, -0.930507)97.441, 101.048, 114.781
117generate(0.785171, -0.600456, 0.151523), (-0.37016, -0.258896, 0.892163), (-0.496475, -0.756588, -0.425542)97.441, 101.048, 114.781
118generate(-0.483048, -0.201044, 0.852201), (0.394824, 0.818705, 0.416938), (-0.781524, 0.53787, -0.316096)97.441, 101.048, 114.781
119generate(0.710295, 0.247908, 0.658804), (-0.247393, -0.788299, 0.563366), (0.658998, -0.56314, -0.498594)97.441, 101.048, 114.781
120generate(-0.999992, -0.003997, 3.0E-6), (-0.003997, 0.99999, -0.001745), (4.0E-6, -0.001745, -0.999998)98.73806, 101.4658, 115.48544

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Components

#1: Protein Porcine circovirus 2 (PCV2) capsid protein / Cap protein / Capsid protein / ORF2


Mass: 26135.219 Da / Num. of mol.: 1 / Fragment: unp residues 42-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine circovirus 2 / Gene: cap, Cap, ORF2, cp / Production host: Escherichia coli (E. coli) / References: UniProt: Q805N7
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.09 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 6% PEG 3350, 2.5% isopropanol, 0.3 M monium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.88 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 11, 2009
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 1002451 / % possible obs: 68.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 5 Å2
Reflection shellResolution: 2.35→2.43 Å / % possible all: 44.8

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.96 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 0.32 / Data cutoff high absF: 129094 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.253 20288 2 %RANDOM
Rwork0.225 ---
obs-728609 68.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 2.8822 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 121.27 Å2 / Biso mean: 26.8697 Å2 / Biso min: 7.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-0.42 Å2-4.59 Å2
2--0.99 Å2-0.79 Å2
3----2.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.35→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 20 128 1742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.35→2.46 Å / Total num. of bins used: 6
Num. reflection% reflection
Rwork72420 -
all72507 -
Rfree-0.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5sulfate.paramsulfate.top

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