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- PDB-1lp3: The Atomic Structure of Adeno-Associated Virus (AAV-2), a Vector ... -

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Basic information

Entry
Database: PDB / ID: 1lp3
TitleThe Atomic Structure of Adeno-Associated Virus (AAV-2), a Vector for Human Gene Therapy
ComponentsAAV-2 capsid protein
KeywordsVIRUS / capsid / single-stranded / DNA / beta-barrel / parvovirus / satellite / human / Icosahedral virus
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / host cell nucleolus / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesAdeno-associated virus - 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement at 15A, then phase extension by symmetry averaging / Resolution: 3 Å
AuthorsXie, Q. / Bu, W. / Bhatia, S. / Hare, J. / Somasundaram, T. / Azzi, A. / Chapman, M.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy.
Authors: Xie, Q. / Bu, W. / Bhatia, S. / Hare, J. / Somasundaram, T. / Azzi, A. / Chapman, M.S.
History
DepositionMay 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Other
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
A: AAV-2 capsid protein


Theoretical massNumber of molelcules
Total (without water)58,7731
Polymers58,7731
Non-polymers00
Water00
1
A: AAV-2 capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,526,35860
Polymers3,526,35860
Non-polymers00
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: AAV-2 capsid protein
x 5


  • icosahedral pentamer
  • 294 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)293,8635
Polymers293,8635
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: AAV-2 capsid protein
x 6


  • icosahedral 23 hexamer
  • 353 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)352,6366
Polymers352,6366
Non-polymers00
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: AAV-2 capsid protein
x 60
A: AAV-2 capsid protein
x 60
A: AAV-2 capsid protein
x 60


  • crystal asymmetric unit, crystal frame
  • 10.6 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)10,579,073180
Polymers10,579,073180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z4
point symmetry operation177
transform to crystal frame2
Unit cell
Length a, b, c (Å)249.690, 249.690, 644.760
Angle α, β, γ (deg.)90.00, 101.16, 120.00
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.99070752, 0.11065694, -0.07908), (-0.10992186, 0.30901719, -0.94468278), (-0.08009863, 0.94459696, 0.31830927)
3generate(0.97567198, 0.06912483, -0.20805276), (-0.06720037, -0.80901648, -0.58393189), (-0.2086823, 0.5837072, -0.78468949)
4generate(0.97567198, -0.06720037, -0.2086823), (0.06912483, -0.80901648, 0.5837072), (-0.20805276, -0.58393189, -0.78468949)
5generate(0.99070752, -0.10992186, -0.08009863), (0.11065694, 0.30901719, 0.94459696), (-0.07908, -0.94468278, 0.31830927)
6generate(0.64123141, -0.00055187, 0.76734736), (-0.00055187, -0.99999981, -0.00025802), (0.76734736, -0.00025802, -0.6412316)
7generate(0.57386998, 0.79562015, 0.19406654), (0.10939577, -0.30932193, 0.94464412), (0.81160693, -0.52087284, -0.26454805)
8generate(0.46553679, 0.49267766, -0.73521712), (0.06671576, 0.80882757, 0.58424907), (0.88251034, -0.32104, 0.34366963)
9generate(0.46594464, -0.49072311, -0.73626519), (-0.06960958, 0.80920408, -0.58338946), (0.88207148, 0.3230783, 0.34288527)
10generate(0.57452988, -0.79555573, 0.19237073), (-0.11118326, -0.30871272, -0.94463471), (0.81089685, 0.52133247, -0.26581716)
11generate(-0.64123168, 0.00128034, -0.76734627), (0.00128034, -0.99999543, -0.00273843), (-0.76734627, -0.00273843, 0.64122711)
12generate(-0.5739504, -0.79539404, -0.19475434), (0.11140915, -0.31146082, 0.94370555), (-0.81127612, 0.51994276, 0.26737723)
13generate(-0.46558623, -0.49326639, 0.73479094), (0.06902071, 0.80750284, 0.58581166), (-0.88230698, 0.32346164, -0.34191661)
14generate(-0.46589477, 0.49013315, 0.7366896), (-0.06730558, 0.8105258, -0.5818229), (-0.88227661, -0.32065157, -0.34463103)
15generate(-0.57444962, 0.79577983, -0.19168225), (-0.10917144, -0.30656957, -0.94556687), (-0.81122699, -0.5222543, 0.2629852)
16generate(-0.99999973, -0.00072847, -1.09E-6), (-0.00072847, 0.99999525, 0.00299646), (-1.09E-6, 0.00299646, -0.99999551)
17generate(-0.9906271, -0.11088305, 0.07976781), (-0.11088305, 0.31176556, -0.94366688), (0.07976781, -0.94366688, -0.32113846)
18generate(-0.97562254, -0.0685361, 0.20847894), (-0.0685361, -0.80731393, -0.58612884), (0.20847894, -0.58612884, 0.78293647)
19generate(-0.97572185, 0.06779033, 0.20825789), (0.06779033, -0.8107134, 0.58150516), (0.20825789, 0.58150516, 0.78643525)
20generate(-0.99078778, 0.10969775, 0.07941015), (0.10969775, 0.3062651, 0.94560462), (0.07941015, 0.94560462, -0.31547731)
21generate(0.38415786, -0.42216806, -0.82109492), (-0.9060058, -0.00120734, -0.42326355), (0.17769701, 0.90651678, -0.38295052)
22generate(0.49276215, -0.86355122, 0.10707357), (-0.86355122, -0.50044238, -0.06194122), (0.10707357, -0.06194122, -0.99231978)
23generate(0.57452988, -0.11118326, 0.81089685), (-0.79555573, -0.30871272, 0.52133247), (0.19237073, -0.94463471, -0.26581716)
24generate(0.51646083, 0.79518888, 0.31771507), (-0.79598678, 0.30901776, 0.5204931), (0.31571073, -0.52171129, 0.7925554)
25generate(0.39880444, 0.6029897, -0.69091131), (-0.86424868, 0.49906654, -0.06329934), (0.30664187, 0.62236325, 0.720163)
26generate(-0.38349795, 0.42216784, 0.82140345), (-0.90574888, 0.00181654, -0.42381089), (-0.18041144, -0.90651587, 0.38168141)
27generate(-0.49213307, 0.86391562, -0.10702733), (-0.86358524, -0.49999653, -0.06499237), (-0.10966122, 0.06044233, 0.9921296)
28generate(-0.5739504, 0.11140915, -0.81127612), (-0.79539404, -0.31146082, 0.51994276), (-0.19475434, 0.94370555, 0.26737723)
29generate(-0.51588118, -0.79541321, -0.31809501), (-0.79541321, 0.30687374, 0.52263404), (-0.31809501, 0.52263404, -0.79099256)
30generate(-0.39817509, -0.60335377, 0.69095646), (-0.86361625, 0.50048979, -0.06063779), (-0.30923061, -0.62086568, -0.72034869)
31generate(0.38318942, 0.4249065, -0.82013434), (0.90574778, 0.00120642, 0.42381542), (0.18107135, -0.90523644, -0.38439583)
32generate(0.39861376, -0.60099042, -0.69276084), (0.86325149, 0.50093483, 0.06213816), (0.3096836, -0.62279596, 0.7184854)
33generate(0.51646083, -0.79598678, 0.31571073), (0.79518888, 0.30901776, -0.52171129), (0.31771507, 0.5204931, 0.7925554)
34generate(0.57386998, 0.10939577, 0.81160693), (0.79562015, -0.30932193, -0.52087284), (0.19406654, 0.94464412, -0.26454805)
35generate(0.49150372, 0.86394931, 0.10961607), (0.86394931, -0.4995598, 0.0634948), (0.10961607, 0.0634948, -0.99194391)
36generate(-0.38384932, -0.42490628, 0.81982581), (0.9060069, -0.00181562, 0.42325902), (-0.17835692, 0.90523553, 0.38566495)
37generate(-0.39924284, 0.60062603, 0.69271461), (0.86388496, 0.49950408, 0.06479543), (-0.30709595, 0.62429485, -0.71829522)
38generate(-0.51704031, 0.79576089, -0.31533146), (0.79576089, 0.31115578, -0.51956394), (-0.31533146, -0.51956394, -0.79411547)
39generate(-0.57444962, -0.10917144, -0.81122699), (0.79577983, -0.30656957, -0.5222543), (-0.19168225, -0.94556687, 0.2629852)
40generate(-0.49213307, -0.86358524, -0.10966122), (0.86391562, -0.49999653, 0.06044233), (-0.10702733, -0.06499237, 0.9921296)
41generate(0.38415786, -0.9060058, 0.17769701), (-0.42216806, -0.00120734, 0.90651678), (-0.82109492, -0.42326355, -0.38295052)
42generate(0.46594464, -0.06960958, 0.88207148), (-0.49072311, 0.80920408, 0.3230783), (-0.73626519, -0.58338946, 0.34288527)
43generate(0.39861376, 0.86325149, 0.3096836), (-0.60099042, 0.50093483, -0.62279596), (-0.69276084, 0.06213816, 0.7184854)
44generate(0.27521421, 0.60339512, -0.74844604), (-0.60058432, -0.49999745, -0.62393992), (-0.75070341, 0.62122209, 0.22478325)
45generate(0.26627997, -0.49006603, -0.83001823), (-0.49006603, -0.81033838, 0.32122733), (-0.83001823, 0.32122733, -0.45594159)
46generate(0.38318942, 0.90574778, 0.18107135), (0.4249065, 0.00120642, -0.90523644), (-0.82013434, 0.42381542, -0.38439583)
47generate(0.26556359, 0.49333365, -0.82831026), (0.49333365, -0.80769193, -0.32288644), (-0.82831026, -0.32288644, -0.45787166)
48generate(0.27521421, -0.60058432, -0.75070341), (0.60339512, -0.49999745, 0.62122209), (-0.74844604, -0.62393992, 0.22478325)
49generate(0.39880444, -0.86424868, 0.30664187), (0.6029897, 0.49906654, 0.62236325), (-0.69091131, -0.06329934, 0.720163)
50generate(0.46553679, 0.06671576, 0.88251034), (0.49267766, 0.80882757, -0.32104), (-0.73521712, 0.58424907, 0.34366963)
51generate(-0.38384932, 0.9060069, -0.17835692), (-0.42490628, -0.00181562, 0.90523553), (0.81982581, 0.42325902, 0.38566495)
52generate(-0.46558623, 0.06902071, -0.88230698), (-0.49326639, 0.80750284, 0.32346164), (0.73479094, 0.58581166, -0.34191661)
53generate(-0.39817509, -0.86361625, -0.30923061), (-0.60335377, 0.50048979, -0.62086568), (0.69095646, -0.06063779, -0.72034869)
54generate(-0.27477581, -0.6030314, 0.74890012), (-0.6030314, -0.49857317, -0.62271818), (0.74890012, -0.62271818, -0.22665103)
55generate(-0.26592199, 0.49065585, 0.82978451), (-0.49274479, -0.80901499, 0.32046424), (0.82854576, -0.3236535, 0.45690299)
56generate(-0.38349795, -0.90574888, -0.18041144), (0.42216784, 0.00181654, -0.90651587), (0.82140345, -0.42381089, 0.38168141)
57generate(-0.26592199, -0.49274479, 0.82854576), (0.49065585, -0.80901499, -0.3236535), (0.82978451, 0.32046424, 0.45690299)
58generate(-0.27565287, 0.60094908, 0.75025043), (0.60094908, -0.50142718, 0.62243955), (0.75025043, 0.62243955, -0.22291995)
59generate(-0.39924284, 0.86388496, -0.30709595), (0.60062603, 0.49950408, 0.62429485), (0.69271461, 0.06479543, -0.71829522)
60generate(-0.46589477, -0.06730558, -0.88227661), (0.49013315, 0.8105258, -0.32065157), (0.7366896, -0.5818229, -0.34463103)
61generate(-0.500001, -0.866029), (0.866031, -0.499999), (1.000002)124.27942, 74.18714, 419.06757
62generate(-0.40015923, -0.32294643, 0.85766277), (0.91294425, -0.05867595, 0.40385471), (-0.08009879, 0.94459885, 0.31830991)124.27942, 74.18714, 419.06757
63generate(-0.4296395, 0.66606925, 0.60972854), (0.87856229, 0.46437167, 0.11178522), (-0.20868272, 0.58370837, -0.78469106)124.27942, 74.18714, 419.06757
64generate(-0.54770107, 0.73423198, -0.40116601), (0.81039983, 0.34630983, -0.47257836), (-0.20805318, -0.58393306, -0.78469106)124.27942, 74.18714, 419.06757
65generate(-0.59118687, -0.21265681, -0.77799897), (0.80265507, -0.24970403, -0.54166543), (-0.07908016, -0.94468467, 0.31830991)124.27942, 74.18714, 419.06757
66generate(-0.32013841, 0.86630477, -0.38345099), (0.55560222, 0.49952097, 0.66467561), (0.76734889, -0.00025802, -0.64123288)124.27942, 74.18714, 419.06757
67generate(-0.38167547, -0.12992911, -0.91512266), (0.44229142, 0.84369237, -0.30425348), (0.81160856, -0.52087388, -0.26454858)124.27942, 74.18714, 419.06757
68generate(-0.29054664, -0.94680745, -0.13836734), (0.36981148, 0.02226116, -0.92884477), (0.88251211, -0.32104065, 0.34367032)124.27942, 74.18714, 419.06757
69generate(-0.17268887, -0.45543215, 0.87336552), (0.43832722, -0.82958266, -0.34593433), (0.88207325, 0.32307895, 0.34288596)124.27942, 74.18714, 419.06757
70generate(-0.19097759, 0.66513283, 0.7218955), (0.55315221, -0.53461987, 0.63891543), (0.81089847, 0.52133351, -0.26581769)124.27942, 74.18714, 419.06757
71generate(0.31950767, 0.86538487, 0.38604546), (-0.55596668, 0.50110553, -0.66317644), (-0.7673478, -0.00273844, 0.64122839)124.27942, 74.18714, 419.06757
72generate(0.19049222, 0.66743192, -0.71989901), (-0.5527633, -0.5331058, -0.64051513), (-0.81127774, 0.5199438, 0.26737777)124.27942, 74.18714, 419.06757
73generate(0.17301964, -0.45268719, -0.8747261), (-0.4377224, -0.8309346, 0.34344649), (-0.88230874, 0.32346229, -0.34191729)124.27942, 74.18714, 419.06757
74generate(0.29123644, -0.94700591, 0.13552997), (-0.36982659, 0.01920841, 0.9289069), (-0.88227838, -0.32065221, -0.34463172)124.27942, 74.18714, 419.06757
75generate(0.38177102, -0.13239258, 0.91472965), (-0.44290557, 0.84245448, 0.30677971), (-0.81122861, -0.52225535, 0.26298573)124.27942, 74.18714, 419.06757
76generate(0.50063174, -0.86566065, -0.00259447), (-0.86566654, -0.5006275, -0.00149917), (-1.09E-6, 0.00299646, -0.99999751)124.27942, 74.18714, 419.06757
77generate(0.59134248, -0.21455638, 0.7773589), (-0.80247236, -0.25191063, 0.54091389), (0.07976797, -0.94366877, -0.3211391)124.27942, 74.18714, 419.06757
78generate(0.5471665, 0.7334254, 0.4033649), (-0.81065138, 0.34430177, 0.47361306), (0.20847935, -0.58613001, 0.78293803)124.27942, 74.18714, 419.06757
79generate(0.42915351, 0.66820608, -0.60772949), (-0.87890046, 0.46406442, -0.11039421), (0.20825831, 0.58150632, 0.78643682)124.27942, 74.18714, 419.06757
80generate(0.40039345, -0.32008344, -0.85862617), (-0.9129017, -0.05813059, -0.40402971), (0.07941031, 0.94560651, -0.31547795)124.27942, 74.18714, 419.06757
81generate(0.59254798, 0.21213004, 0.77710679), (0.78569461, -0.36500696, -0.4994623), (0.17769737, 0.90651859, -0.38295129)124.27942, 74.18714, 419.06757
82generate(0.50147883, 0.86517409, 0.000106), (0.85852205, -0.49764144, 0.12369958), (0.10707378, -0.06194134, -0.99232176)124.27942, 74.18714, 419.06757
83generate(0.40170881, 0.32294591, -0.85693827), (0.89533776, 0.05806791, 0.44159609), (0.19237112, -0.9446366, -0.26581769)124.27942, 74.18714, 419.06757
84generate(0.43111671, -0.66521358, -0.60961997), (0.84526368, 0.53414965, 0.01490507), (0.31571136, -0.52171234, 0.79255699)124.27942, 74.18714, 419.06757
85generate(0.5490618, -0.73370155, 0.40027541), (0.77750049, 0.272675, -0.56670101), (0.30664248, 0.62236449, 0.72016444)124.27942, 74.18714, 419.06757
86generate(0.97615416, -0.21265752, -0.04367003), (0.12075242, 0.36470217, 0.92326587), (-0.1804118, -0.90651768, 0.38168217)124.27942, 74.18714, 419.06757
87generate(0.99395688, 0.00105282, 0.10979905), (0.00558926, 0.99817547, -0.06019287), (-0.10966144, 0.06044245, 0.99213158)124.27942, 74.18714, 419.06757
88generate(0.97581008, 0.21402942, -0.04464664), (-0.09936262, 0.25221387, -0.96256113), (-0.19475473, 0.94370744, 0.26737777)124.27942, 74.18714, 419.06757
89generate(0.94679201, 0.13194584, -0.29356841), (-0.04906329, -0.84228906, -0.53679664), (-0.31809565, 0.52263508, -0.79099414)124.27942, 74.18714, 419.06757
90generate(0.94700466, -0.13176119, -0.29296483), (0.08697529, -0.77276747, 0.62870855), (-0.30923123, -0.62086692, -0.72035013)124.27942, 74.18714, 419.06757
91generate(-0.97599893, -0.21349847, 0.04303155), (-0.12101907, 0.36737899, -0.92216905), (0.18107171, -0.90523825, -0.3843966)124.27942, 74.18714, 419.06757
92generate(-0.94690811, -0.13332828, 0.29256767), (-0.08641301, -0.77094325, -0.63102138), (0.30968422, -0.6227972, 0.71848683)124.27942, 74.18714, 419.06757
93generate(-0.94688756, 0.13037584, 0.29396143), (0.04967744, -0.8438578, 0.5342704), (0.3177157, 0.52049414, 0.79255699)124.27942, 74.18714, 419.06757
94generate(-0.97596569, 0.21318377, 0.04528671), (0.09917991, 0.24940078, 0.96331266), (0.19406693, 0.94464601, -0.26454858)124.27942, 74.18714, 419.06757
95generate(-0.99395751, 0.00065776, -0.10979649), (-0.00631634, 0.99798629, 0.06318358), (0.10961629, 0.06349493, -0.9919459)124.27942, 74.18714, 419.06757
96generate(-0.59270321, 0.21402595, -0.77646831), (-0.78542796, -0.3670742, 0.49836548), (-0.17835728, 0.90523734, 0.38566572)124.27942, 74.18714, 419.06757
97generate(-0.54852761, -0.73289863, -0.40247272), (-0.7776983, 0.27040922, 0.56751467), (-0.30709656, 0.62429609, -0.71829666)124.27942, 74.18714, 419.06757
98generate(-0.43063134, -0.66735117, 0.60762348), (-0.84565258, 0.53357602, -0.01330537), (-0.31533209, -0.51956498, -0.79411706)124.27942, 74.18714, 419.06757
99generate(-0.40194303, 0.32008396, 0.85790168), (-0.8953803, 0.05873863, -0.44142109), (-0.19168264, -0.94556876, 0.26298573)124.27942, 74.18714, 419.06757
100generate(-0.50210895, 0.86480498, 0.00248591), (-0.85815944, -0.49789382, -0.12519112), (-0.10702755, -0.0649925, 0.99213158)124.27942, 74.18714, 419.06757
101generate(0.17353047, 0.45404939, -0.8739185), (0.54377622, -0.78402544, -0.29936636), (-0.82109656, -0.42326439, -0.38295129)124.27942, 74.18714, 419.06757
102generate(0.19200766, -0.66598934, -0.7208318), (0.64888356, -0.46488528, 0.60236242), (-0.73626666, -0.58339063, 0.34288596)124.27942, 74.18714, 419.06757
103generate(0.32116786, -0.8654507, 0.38451725), (0.64570648, 0.49713564, 0.57959295), (-0.69276223, 0.06213828, 0.71848683)124.27942, 74.18714, 419.06757
104generate(0.38251606, 0.13131413, 0.91457383), (0.5386356, 0.7725571, -0.33620814), (-0.75070491, 0.62122333, 0.2247837)124.27942, 74.18714, 419.06757
105generate(0.29127114, 0.94681004, 0.13681776), (0.47563923, -0.01924399, -0.87943487), (-0.83001989, 0.32122798, -0.4559425)124.27942, 74.18714, 419.06757
106generate(-0.55957644, -0.45391959, 0.69342515), (0.11940109, 0.78380245, 0.60943071), (-0.82013598, 0.42381626, -0.3843966)124.27942, 74.18714, 419.06757
107generate(-0.56002331, 0.45281732, 0.69378498), (-0.01668003, 0.83108739, -0.55589947), (-0.82831192, -0.32288709, -0.45787257)124.27942, 74.18714, 419.06757
108generate(-0.66016505, 0.73330506, -0.16264389), (-0.06335292, -0.27012642, -0.96074285), (-0.74844754, -0.62394116, 0.2247837)124.27942, 74.18714, 419.06757
109generate(-0.72160918, -8.089E-5, -0.69230586), (0.04388276, -0.99799892, -0.04561964), (-0.69091269, -0.06329947, 0.72016444)124.27942, 74.18714, 419.06757
110generate(-0.65944201, -0.73382608, -0.1632261), (0.15683095, -0.34663506, 0.92480099), (-0.73521859, 0.58425024, 0.34367032)124.27942, 74.18714, 419.06757
111generate(0.5599062, -0.45143198, -0.69478158), (-0.1199727, 0.78553787, -0.60707948), (0.81982745, 0.42325987, 0.38566572)124.27942, 74.18714, 419.06757
112generate(0.65997658, -0.7338313, 0.16102721), (-0.15657941, -0.34397653, -0.92583569), (0.73479241, 0.58581284, -0.34191729)124.27942, 74.18714, 419.06757
113generate(0.72160981, -0.00162969, 0.6923033), (-0.04315569, -0.99816284, 0.04262892), (0.69095784, -0.06063791, -0.72035013)124.27942, 74.18714, 419.06757
114generate(0.65963086, 0.73329512, 0.16484119), (0.06355073, -0.2729578, 0.95992918), (0.74890161, -0.62271942, -0.22665148)124.27942, 74.18714, 419.06757
115generate(0.55969254, 0.45530202, -0.69242441), (0.01607521, 0.82942986, 0.55838731), (0.82854741, -0.32365415, 0.4569039)124.27942, 74.18714, 419.06757
116generate(-0.17386023, 0.45130217, 0.87527493), (-0.54320461, -0.78531488, 0.29701512), (0.8214051, -0.42381173, 0.38168217)124.27942, 74.18714, 419.06757
117generate(-0.29196093, 0.94700332, -0.13398039), (-0.47562413, -0.02222558, 0.87937274), (0.82978617, 0.32046488, 0.4569039)124.27942, 74.18714, 419.06757
118generate(-0.38261262, 0.13377534, -0.91417666), (-0.53919787, 0.77115362, 0.33852097), (0.75025193, 0.6224408, -0.2229204)124.27942, 74.18714, 419.06757
119generate(-0.32053774, -0.86452836, -0.38710916), (-0.64606909, 0.49839962, -0.57810141), (0.69271599, 0.06479556, -0.71829666)124.27942, 74.18714, 419.06757
120generate(-0.19152167, -0.66828599, 0.71883275), (-0.64854539, -0.46355081, -0.60375343), (0.73669107, -0.58182407, -0.34463172)124.27942, 74.18714, 419.06757
121generate(-0.5, 0.866029), (-0.866031, -0.5), (1.000002)-2.1089, 144.7227, 209.53378
122generate(-0.59054928, 0.21228938, -0.77858268), (-0.8030225, -0.25034094, 0.54082713), (-0.08009879, 0.94459885, 0.31830991)-2.1089, 144.7227, 209.53378
123generate(-0.54603346, -0.73519414, -0.40167557), (-0.81136199, 0.34464399, 0.47214608), (-0.20868272, 0.58370837, -0.78469106)-2.1089, 144.7227, 209.53378
124generate(-0.42797188, -0.66703155, 0.60984852), (-0.87952459, 0.46270584, -0.11112826), (-0.20805318, -0.58393306, -0.78469106)-2.1089, 144.7227, 209.53378
125generate(-0.39952164, 0.32257878, 0.85809767), (-0.9133119, -0.05931286, -0.40293059), (-0.07908016, -0.94468467, 0.31830991)-2.1089, 144.7227, 209.53378
126generate(-0.32109364, -0.86575291, -0.38389713), (-0.55505035, 0.50047784, -0.66441759), (0.76734889, -0.00025802, -0.64123288)-2.1089, 144.7227, 209.53378
127generate(-0.19219508, -0.66569184, 0.72105593), (-0.55168708, -0.53437075, -0.6403897), (0.81160856, -0.52087388, -0.26454858)-2.1089, 144.7227, 209.53378
128generate(-0.17499062, 0.4541293, 0.8735852), (-0.43652717, -0.83108791, 0.34459628), (0.88251211, -0.32104065, 0.34367032)-2.1089, 144.7227, 209.53378
129generate(-0.29325623, 0.94615575, -0.1370996), (-0.36871771, 0.02037939, 0.92932321), (0.88207325, 0.32307895, 0.34288596)-2.1089, 144.7227, 209.53378
130generate(-0.38355287, 0.13042369, -0.91426642), (-0.44196906, 0.84333228, 0.30571834), (0.81089847, 0.52133351, -0.26581769)-2.1089, 144.7227, 209.53378
131generate(0.32172465, -0.86666521, 0.38130157), (0.55468634, 0.4988889, 0.66591487), (-0.7673478, -0.00273844, 0.64122839)-2.1089, 144.7227, 209.53378
132generate(0.38345875, 0.12796292, 0.91465354), (0.44135427, 0.84456631, -0.30318948), (-0.81127774, 0.5199438, 0.26737777)-2.1089, 144.7227, 209.53378
133generate(0.29256706, 0.94595407, 0.13993442), (0.36870175, 0.02343257, -0.92925757), (-0.88230874, 0.32346229, -0.34191729)-2.1089, 144.7227, 209.53378
134generate(0.1746588, 0.45687227, -0.8722203), (0.4371321, -0.8297334, -0.34708458), (-0.88227838, -0.32065221, -0.34463172)-2.1089, 144.7227, 209.53378
135generate(0.19267918, -0.66338805, -0.7230472), (0.5520769, -0.53588522, 0.63878621), (-0.81122861, -0.52225535, 0.26298573)-2.1089, 144.7227, 209.53378
136generate(0.49936899, 0.86638912, 0.00259556), (0.86639501, -0.49936674, -0.00149728), (-1.09E-6, 0.00299646, -0.99999751)-2.1089, 144.7227, 209.53378
137generate(0.39928561, 0.32543954, -0.85712679), (0.9133553, -0.05985462, 0.40275205), (0.07976797, -0.94366877, -0.3211391)-2.1089, 144.7227, 209.53378
138generate(0.42845702, -0.66488923, -0.61184404), (0.87918741, 0.46301136, 0.1125152), (0.20847935, -0.58613001, 0.78293803)-2.1089, 144.7227, 209.53378
139generate(0.54656932, -0.73599648, 0.39947139), (0.8111102, 0.34664817, -0.47111037), (0.20825831, 0.58150632, 0.78643682)-2.1089, 144.7227, 209.53378
140generate(0.59039533, 0.21038558, 0.77921595), (0.80320406, -0.2481342, -0.54157396), (0.07941031, 0.94560651, -0.31547795)-2.1089, 144.7227, 209.53378
141generate(-0.97670623, 0.21003844, 0.04398895), (0.12031029, 0.3662143, 0.92272543), (0.17769737, 0.90651859, -0.38295129)-2.1089, 144.7227, 209.53378
142generate(-0.99424148, -0.001622, -0.10717968), (0.00502831, 0.99808332, -0.06175842), (0.10707378, -0.06194134, -0.99232176)-2.1089, 144.7227, 209.53378
143generate(-0.97623927, -0.21176254, 0.04604061), (-0.09978283, 0.25064451, -0.96292804), (0.19237112, -0.9446366, -0.26581769)-2.1089, 144.7227, 209.53378
144generate(-0.94757805, -0.1299761, 0.29190459), (-0.0492777, -0.8431671, -0.53539765), (0.31571136, -0.52171234, 0.79255699)-2.1089, 144.7227, 209.53378
145generate(-0.94786664, 0.13071125, 0.29063659), (0.08674733, -0.77174104, 0.63000028), (0.30664248, 0.62236449, 0.72016444)-2.1089, 144.7227, 209.53378
146generate(-0.59265582, -0.20951074, -0.77773425), (0.78499555, -0.36651871, -0.49945541), (-0.1804118, -0.90651768, 0.38168217)-2.1089, 144.7227, 209.53378
147generate(-0.50182332, -0.8649693, -0.00277161), (0.85799511, -0.49817944, 0.12518517), (-0.10966144, 0.06044245, 0.99213158)-2.1089, 144.7227, 209.53378
148generate(-0.4018591, -0.32543867, 0.85592357), (0.89475586, 0.05924664, 0.44261888), (-0.19475473, 0.94370744, 0.26737777)-2.1089, 144.7227, 209.53378
149generate(-0.43091031, 0.66346816, 0.61166374), (0.8444757, 0.53541563, 0.01416312), (-0.31809565, 0.52263508, -0.79099414)-2.1089, 144.7227, 209.53378
150generate(-0.54882917, 0.73511556, -0.39799232), (0.7766401, 0.27227817, -0.56807081), (-0.30923123, -0.62086692, -0.72035013)-2.1089, 144.7227, 209.53378
151generate(0.59280913, -0.21140846, 0.77710361), (-0.7847278, -0.36858541, 0.49835406), (0.18107171, -0.90523825, -0.3843966)-2.1089, 144.7227, 209.53378
152generate(0.54829395, 0.73431931, 0.40019387), (-0.77683762, 0.27000892, 0.56888328), (0.30968422, -0.6227972, 0.71848683)-2.1089, 144.7227, 209.53378
153generate(0.43042622, 0.66561173, -0.60967247), (-0.84486552, 0.53484035, -0.01255963), (0.3177157, 0.52049414, 0.79255699)-2.1089, 144.7227, 209.53378
154generate(0.40209514, -0.32257965, -0.85689445), (-0.89479927, 0.05992084, -0.44244034), (0.19406693, 0.94464601, -0.26454858)-2.1089, 144.7227, 209.53378
155generate(0.5024533, -0.86460793, 0.0001803), (-0.85763211, -0.49842698, -0.12667832), (0.10961629, 0.06349493, -0.9919459)-2.1089, 144.7227, 209.53378
156generate(0.97655291, 0.21088076, -0.04335832), (-0.12057804, 0.36888982, -0.92162407), (-0.17835728, 0.90523734, 0.38566572)-2.1089, 144.7227, 209.53378
157generate(0.94777085, 0.132272, -0.29024258), (-0.0861858, -0.7699128, -0.63231004), (-0.30709656, 0.62429609, -0.71829666)-2.1089, 144.7227, 209.53378
158generate(0.94767216, -0.12841052, -0.29229171), (0.04989249, -0.84473149, 0.53286879), (-0.31533209, -0.51956498, -0.79411706)-2.1089, 144.7227, 209.53378
159generate(0.97639323, -0.21091242, -0.04667388), (0.09960126, 0.24783063, 0.96367487), (-0.19168264, -0.94556876, 0.26298573)-2.1089, 144.7227, 209.53378
160generate(0.99424251, -0.00121888, 0.10717542), (-0.00575532, 0.99788985, 0.06474885), (-0.10702755, -0.0649925, 0.99213158)-2.1089, 144.7227, 209.53378
161generate(-0.55768871, 0.45195731, 0.69622131), (-0.12160858, 0.78523278, -0.60714951), (-0.82109656, -0.42326439, -0.38295129)-2.1089, 144.7227, 209.53378
162generate(-0.65795276, 0.73559899, -0.16124057), (-0.15816094, -0.34431799, -0.9254404), (-0.73626666, -0.58339063, 0.34288596)-2.1089, 144.7227, 209.53378
163generate(-0.71978201, 0.00219835, -0.69420116), (-0.04471666, -0.99806997, 0.04320238), (-0.69276223, 0.06213828, 0.71848683)-2.1089, 144.7227, 209.53378
164generate(-0.65773054, -0.73470985, -0.16612704), (0.06194813, -0.27256015, 0.96014743), (-0.75070491, 0.62122333, 0.2247837)-2.1089, 144.7227, 209.53378
165generate(-0.55755137, -0.45674352, 0.6932013), (0.01442631, 0.82958156, 0.55820785), (-0.83001989, 0.32122798, -0.4559425)-2.1089, 144.7227, 209.53378
166generate(0.17638664, -0.4518291, -0.87449668), (-0.54430716, -0.78500886, 0.29580482), (-0.82013598, 0.42381626, -0.3843966)-2.1089, 144.7227, 209.53378
167generate(0.29445945, -0.94615146, 0.13452611), (-0.47665312, -0.02339627, 0.87878559), (-0.82831192, -0.32288709, -0.45787257)-2.1089, 144.7227, 209.53378
168generate(0.38495057, -0.13272013, 0.91334805), (-0.54004159, 0.77012337, 0.33952138), (-0.74844754, -0.62394116, 0.2247837)-2.1089, 144.7227, 209.53378
169generate(0.32280434, 0.86433044, 0.38566369), (-0.64687186, 0.49893288, -0.57674299), (-0.69091269, -0.06329947, 0.72016444)-2.1089, 144.7227, 209.53378
170generate(0.19390475, 0.66711025, -0.71928512), (-0.64950813, -0.4621917, -0.60376131), (-0.73521859, 0.58425024, 0.34367032)-2.1089, 144.7227, 209.53378
171generate(-0.1760565, -0.45457583, 0.87313868), (0.54487855, -0.78372225, -0.29815514), (0.81982745, 0.42325987, 0.38566572)-2.1089, 144.7227, 209.53378
172generate(-0.19438988, 0.66481052, 0.72128065), (0.64984531, -0.4635255, 0.60237437), (0.73479241, 0.58581284, -0.34191729)-2.1089, 144.7227, 209.53378
173generate(-0.32343432, 0.8652468, -0.38307238), (0.64650886, 0.49767355, 0.57823614), (0.69095784, -0.06063791, -0.72035013)-2.1089, 144.7227, 209.53378
174generate(-0.38485478, -0.13026312, -0.91374206), (0.53948007, 0.77153047, -0.33721163), (0.74890161, -0.62271942, -0.22665148)-2.1089, 144.7227, 209.53378
175generate(-0.29377028, -0.94595837, -0.13736093), (0.47666908, -0.02041569, -0.87885123), (0.82854741, -0.32365415, 0.4569039)-2.1089, 144.7227, 209.53378
176generate(0.55735857, 0.45444762, -0.69486331), (0.12103719, 0.78349834, 0.60949983), (0.8214051, -0.42381173, 0.38168217)-2.1089, 144.7227, 209.53378
177generate(0.55788319, -0.45425805, -0.69456619), (-0.01503124, 0.83123975, -0.55571956), (0.82978617, 0.32046488, 0.4569039)-2.1089, 144.7227, 209.53378
178generate(0.65826576, -0.73472501, 0.16392549), (-0.06175061, -0.26972694, -0.9609599), (0.75025193, 0.6224408, -0.2229204)-2.1089, 144.7227, 209.53378
179generate(0.71978098, 0.00064253, 0.69420541), (0.04544366, -0.9979032, -0.04619281), (0.69271599, 0.06479556, -0.71829666)-2.1089, 144.7227, 209.53378
180generate(0.6574169, 0.73559164, 0.16344475), (0.15841274, -0.34697418, 0.92440468), (0.73669107, -0.58182407, -0.34463172)-2.1089, 144.7227, 209.53378

-
Components

#1: Protein AAV-2 capsid protein / major coat protein VP2


Mass: 58772.625 Da / Num. of mol.: 1 / Fragment: Residues 80-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 2 / Genus: Dependovirus / Plasmid: pAV2 / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03135

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 6000, magnesium chloride, hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.5 mg/mlprotein1drop
225 %glycerol1drop
34-5 %PEG60001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 1998
RadiationMonochromator: 0.92 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→39.8 Å / Num. obs: 1462541 / % possible obs: 56 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 38.676 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 6.3
Reflection shellResolution: 3.43→3.56 Å / Redundancy: 2 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 5.9 / Num. unique all: 25132 / % possible all: 43
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 100 Å / Num. obs: 495356 / % possible obs: 56 % / Num. measured all: 747988
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.5 Å / % possible obs: 80 %

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Processing

Software
NameClassification
GLRFphasing
RAVEmodel building
CCP4model building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing
CCP4phasing
RefinementMethod to determine structure: Molecular replacement at 15A, then phase extension by symmetry averaging
Starting model: PDB entries 4dpv, 1dnv

4dpv

1dnv


Resolution: 3→39.8 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.342 7117 -Random
Rwork0.338 ---
all0.339 ---
obs0.338 1462541 56 %-
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.076 Å2-6.626 Å2-
2----3.166 Å2
3----8.503 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.67 Å
Luzzati d res low-5 Å
Luzzati sigma a0.89 Å0.94 Å
Refinement stepCycle: LAST / Resolution: 3→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 0 0 4152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_dihedral_angle_d26.68
X-RAY DIFFRACTIONc_improper_angle_d1.68
LS refinement shellResolution: 3.3→3.51 Å
RfactorNum. reflection
Rfree0.4274 546
Rwork0.4164 -
obs-101467
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.68
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.68

+
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