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- PDB-4ang: Small RNA phage PRR1 in complex with an RNA operator fragment -

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Basic information

Entry
Database: PDB / ID: 4ang
TitleSmall RNA phage PRR1 in complex with an RNA operator fragment
Components
  • 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
  • COAT PROTEIN
KeywordsVIRUS / CAPSID / CAPSID PROTEINS / IONS / METALS
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / RNA binding
Similarity search - Function
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Capsid protein
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PRR1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPersson, M. / Tars, K. / Liljas, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Prr1 Coat Protein Binding to its RNA Translational Operator
Authors: Persson, M. / Tars, K. / Liljas, L.
History
DepositionMar 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
S: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5596
Polymers56,5195
Non-polymers401
Water00
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
S: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,393,560360
Polymers3,391,156300
Non-polymers2,40560
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: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
S: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
hetero molecules
x 5


  • icosahedral pentamer
  • 283 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)282,79730
Polymers282,59625
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
S: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 339 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)339,35636
Polymers339,11630
Non-polymers2406
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: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
S: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
hetero molecules
x 60
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
S: 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 6.79 MDa, 600 polymers
Theoretical massNumber of molelcules
Total (without water)6,787,121720
Polymers6,782,311600
Non-polymers4,809120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
point symmetry operation118
transform to crystal frame1
Unit cell
Length a, b, c (Å)281.300, 285.400, 472.900
Angle α, β, γ (deg.)93.23, 90.03, 119.45
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(0.781097, -0.606879, 0.14692), (-0.398183, -0.302874, 0.865862), (-0.480975, -0.734824, -0.478223)
3generate(0.781097, -0.398183, -0.480975), (-0.606879, -0.302874, -0.734824), (0.14692, 0.865862, -0.478223)
4generate(0.977377, -0.013546, -0.21107), (-0.013546, -0.999907, 0.001446), (-0.21107, 0.001446, -0.97747)
5generate(0.870339, -0.433948, 0.232806), (0.386871, 0.310004, -0.868463), (0.304697, 0.845924, 0.43769)
6generate(0.740637, -0.56783, -0.359202), (0.596454, 0.309492, 0.740579), (-0.309353, -0.762748, 0.567905)
7generate(0.506052, 0.316648, 0.802275), (0.30728, 0.802948, -0.510738), (-0.80591, 0.504983, 0.309034)
8generate(-0.116683, -0.992547, -0.035144), (0.165947, -0.054372, 0.984635), (-0.979207, 0.109058, 0.171055)
9generate(0.320979, 0.397253, -0.859746), (-0.322314, -0.807775, -0.493573), (-0.890554, 0.435534, -0.131238)
10generate(0.320979, -0.322314, -0.890554), (0.397253, -0.807775, 0.435534), (-0.859746, -0.493573, -0.131238)
11generate(0.80739, 0.557225, 0.193962), (0.422455, -0.316471, -0.84934), (-0.41189, 0.767688, -0.490918)
12generate(0.315481, -0.801285, 0.508345), (0.864503, 0.463587, 0.19422), (-0.391288, 0.378193, 0.838966)
13generate(-0.293173, 0.819628, 0.492199), (0.813838, 0.484112, -0.321408), (-0.501714, 0.306342, -0.808973)
14generate(-0.792094, -0.432003, 0.431231), (0.597511, -0.404348, 0.692448), (-0.124772, 0.806149, 0.578408)
15generate(-0.654098, 0.294669, -0.696654), (0.294669, -0.748977, -0.593468), (-0.696654, -0.593468, 0.403074)
16generate(-0.401531, -0.814869, -0.418044), (0.856709, -0.495556, 0.14309), (-0.323764, -0.300687, 0.897086)
17generate(0.211902, 0.797672, -0.564639), (0.797672, -0.474973, -0.371644), (-0.564639, -0.371644, -0.736929)
18generate(0.119473, 0.044717, 0.99183), (0.990938, -0.06714, -0.116339), (0.061389, 0.996741, -0.052333)
19generate(-0.293173, 0.813838, -0.501714), (0.819628, 0.484112, 0.306342), (0.492199, -0.321408, -0.808973)
20generate(-0.311741, 0.300101, 0.90153), (0.300101, -0.869147, 0.393094), (0.90153, 0.393094, 0.180888)
21generate(-0.796609, -0.564169, -0.217087), (0.39142, -0.207737, -0.896457), (0.460656, -0.799098, 0.386313)
22generate(-0.191668, -0.810517, 0.553467), (0.729869, -0.494726, -0.471739), (0.656167, 0.313541, 0.686394)
23generate(-0.093181, -0.044897, -0.994636), (0.993985, 0.053543, -0.095536), (0.057545, -0.997556, 0.039638)
24generate(0.42349, 0.80103, 0.423094), (0.80103, -0.549243, 0.238084), (0.423094, 0.238084, -0.874247)
25generate(0.506052, 0.30728, -0.80591), (0.316648, 0.802948, 0.504983), (0.802275, -0.510738, 0.309034)
26generate(0.660544, 0.192022, 0.725816), (-0.315272, -0.806433, 0.50027), (0.681385, -0.55928, -0.472145)
27generate(0.09039, -0.992375, -0.08379), (-0.165767, 0.067969, -0.98382), (0.982014, 0.102817, -0.158359)
28generate(0.660544, -0.315272, 0.681385), (0.192022, -0.806433, -0.55928), (0.725816, 0.50027, -0.472145)
29generate(0.313756, -0.80608, -0.501789), (0.740096, 0.538685, -0.402587), (0.594824, -0.245057, 0.765592)
30generate(0.80739, 0.422455, -0.41189), (0.557225, -0.316471, 0.767688), (0.193962, -0.84934, -0.490918)
31generate(-0.977727, -0.012847, 0.209488), (-0.012847, -0.99259, -0.120834), (0.209488, -0.120834, 0.970316)
32generate(-0.859343, 0.443316, -0.254953), (0.443316, 0.397218, -0.803548), (-0.254953, -0.803548, -0.537875)
33generate(-0.725125, 0.574594, 0.379521), (0.574594, 0.20112, 0.793343), (0.379521, 0.793343, -0.475995)
34generate(-0.99965, 0.026393, 0.001581), (0.026393, 0.992497, 0.119388), (0.001581, 0.119388, -0.992846)
35generate(-0.792094, 0.597511, -0.124772), (-0.432003, -0.404348, 0.806149), (0.431231, 0.692448, 0.578408)
36generate(-0.796609, 0.39142, 0.460656), (-0.564169, -0.207737, -0.799098), (-0.217087, -0.896457, 0.386312)
37generate(-0.667557, -0.214123, -0.713105), (-0.214123, -0.862085, 0.459304), (-0.713105, 0.459304, 0.529642)
38generate(-0.093181, 0.993985, 0.057545), (-0.044897, 0.053543, -0.997556), (-0.994636, -0.095536, 0.039638)
39generate(-0.496249, -0.286789, 0.819445), (0.423411, 0.744058, 0.516819), (-0.757932, 0.603432, -0.247809)
40generate(-0.49904, 0.222115, 0.83763), (-0.294547, 0.86557, -0.405008), (-0.814986, -0.448836, -0.36653)
41generate(-0.88112, -0.379927, -0.281572), (-0.379927, 0.214205, 0.899873), (-0.281572, 0.899873, -0.333085)
42generate(-0.401531, 0.856709, -0.323764), (-0.814869, -0.495556, -0.300687), (-0.418044, 0.14309, 0.897086)
43generate(0.171084, -0.743417, -0.646577), (-0.743417, -0.528071, 0.410454), (-0.646577, 0.410454, -0.643013)
44generate(0.740637, 0.596454, -0.309353), (-0.56783, 0.309492, -0.762748), (-0.359202, 0.740579, 0.567905)
45generate(0.489802, -0.402808, 0.773201), (-0.199902, 0.811352, 0.549316), (-0.848606, -0.423621, 0.31688)
46generate(0.313756, 0.740096, 0.594824), (-0.80608, 0.538685, -0.245057), (-0.501789, -0.402587, 0.765592)
47generate(-0.335715, -0.851658, 0.402459), (-0.726256, 0.506113, 0.46519), (-0.599873, -0.136117, -0.788432)
48generate(-0.116683, 0.165947, -0.979207), (-0.992547, -0.054372, 0.109058), (-0.035144, 0.984635, 0.171055)
49generate(0.379223, -0.869262, 0.317134), (-0.869262, -0.452143, -0.199875), (0.317134, -0.199875, -0.92708)
50generate(0.489802, -0.199902, -0.848606), (-0.402807, 0.811352, -0.42362), (0.773201, 0.549315, 0.31688)
51generate(0.870339, 0.386871, 0.304697), (-0.433948, 0.310004, 0.845924), (0.232806, -0.868463, 0.43769)
52generate(0.315481, 0.864503, -0.391288), (-0.801285, 0.463587, 0.378193), (0.508345, 0.19422, 0.838966)
53generate(0.09039, -0.165767, 0.982014), (-0.992375, 0.067969, 0.102817), (-0.08379, -0.98382, -0.158359)
54generate(-0.335715, -0.726256, -0.599873), (-0.851658, 0.506113, -0.136117), (0.402459, 0.46519, -0.788432)
55generate(-0.330782, -0.417745, 0.846211), (-0.417745, -0.739231, -0.528229), (0.846211, -0.528229, 0.070013)
56generate(-0.49904, -0.294547, -0.814986), (0.222115, 0.86557, -0.448836), (0.83763, -0.405008, -0.36653)
57generate(0.119473, 0.990938, 0.061389), (0.044717, -0.06714, 0.996741), (0.99183, -0.116339, -0.052333)
58generate(-0.496249, 0.423411, -0.757932), (-0.286788, 0.744058, 0.603432), (0.819445, 0.516819, -0.247809)
59generate(-0.191668, 0.729869, 0.656167), (-0.810517, -0.494726, 0.313541), (0.553467, -0.471739, 0.686394)
60generate(-0.755933, -0.586906, 0.290012), (-0.586906, 0.411328, -0.697388), (0.290012, -0.697388, -0.655395)
61generate(0.978815, -0.013544, -0.204298), (0.013429, 0.999908, -0.001949), (0.204306, -0.000836, 0.978907)141.95, -30.15, 234.9
62generate(0.868205, -0.439797, 0.22978), (-0.38672, -0.309564, 0.868687), (-0.310914, -0.843059, -0.438843)141.95, -30.15, 234.9
63generate(0.742754, -0.56254, -0.363133), (-0.59662, -0.309881, -0.740283), (0.30391, 0.7665, -0.565788)141.95, -30.15, 234.9
64generate(0.999976, -1.2E-5, -0.006922), (-8.0E-6, -1, 0.000517), (-0.006922, -0.000517, -0.999976)141.95, -30.15, 234.9
65generate(0.784413, -0.601774, 0.150217), (0.397929, 0.302499, -0.86611), (0.475762, 0.739163, 0.476747)141.95, -30.15, 234.9
66generate(0.780069, -0.404164, -0.477645), (0.606948, 0.303325, 0.73458), (-0.15201, -0.862928, 0.481921)141.95, -30.15, 234.9
67generate(0.655815, 0.195898, 0.729061), (0.315618, 0.806142, -0.500519), (-0.685778, 0.558353, 0.466851)141.95, -30.15, 234.9
68generate(0.083592, -0.993064, -0.082681), (0.166274, -0.067908, 0.983739), (-0.98253, -0.09598, 0.159444)141.95, -30.15, 234.9
69generate(0.500483, 0.310799, -0.808035), (-0.316238, -0.803214, -0.504817), (-0.805922, 0.508183, -0.303708)141.95, -30.15, 234.9
70generate(0.484443, -0.203709, -0.850775), (0.403203, -0.811066, 0.423791), (-0.776365, -0.548337, -0.310779)141.95, -30.15, 234.9
71generate(0.868712, 0.39287, 0.30165), (0.434061, -0.310456, -0.8457), (-0.238601, 0.865604, -0.440226)141.95, -30.15, 234.9
72generate(0.377028, -0.867852, 0.323546), (0.869423, 0.452047, 0.199393), (-0.319302, 0.206121, 0.924965)141.95, -30.15, 234.9
73generate(-0.195485, 0.733123, 0.651396), (0.810804, 0.494477, -0.313192), (-0.551708, 0.46693, -0.691082)141.95, -30.15, 234.9
74generate(-0.757915, -0.582069, 0.29455), (0.587062, -0.411683, 0.697047), (-0.284469, 0.701222, 0.653732)141.95, -30.15, 234.9
75generate(-0.501906, 0.419814, -0.756205), (0.287216, -0.743794, -0.603554), (-0.815841, -0.520122, 0.252738)141.95, -30.15, 234.9
76generate(-0.338483, -0.729465, -0.594399), (0.851869, -0.505867, 0.135714), (-0.399686, -0.460413, 0.792636)141.95, -30.15, 234.9
77generate(0.311964, 0.863133, -0.39709), (0.801545, -0.463493, -0.377756), (-0.510102, -0.200439, -0.836433)141.95, -30.15, 234.9
78generate(0.090979, -0.158953, 0.983085), (0.992331, -0.068476, -0.102907), (0.083675, 0.984909, 0.151504)141.95, -30.15, 234.9
79generate(-0.398618, 0.855703, -0.329963), (0.814656, 0.495623, 0.301153), (0.421235, -0.148761, -0.894668)141.95, -30.15, 234.9
80generate(-0.493383, 0.225207, 0.840152), (0.29413, -0.865803, 0.404811), (0.818573, 0.446841, 0.360932)141.95, -30.15, 234.9
81generate(-0.879146, -0.38615, -0.27927), (0.379788, -0.213737, -0.900043), (0.287861, -0.897332, 0.334561)141.95, -30.15, 234.9
82generate(-0.331546, -0.850702, 0.407902), (0.725949, -0.506176, -0.465601), (0.602558, 0.141748, 0.785386)141.95, -30.15, 234.9
83generate(-0.116425, 0.159128, -0.980369), (0.99253, 0.054879, -0.108962), (0.036463, -0.985732, -0.164328)141.95, -30.15, 234.9
84generate(0.317232, 0.742859, 0.589513), (0.805818, -0.538899, 0.245448), (0.500021, 0.397176, -0.769565)141.95, -30.15, 234.9
85generate(0.327139, 0.394238, -0.858811), (0.321851, 0.807996, 0.493512), (0.888477, -0.437856, 0.137441)141.95, -30.15, 234.9
86generate(0.511615, 0.313136, 0.800122), (-0.307701, -0.80269, 0.510891), (0.802228, -0.507578, -0.314316)141.95, -30.15, 234.9
87generate(-0.109903, -0.993278, -0.036338), (-0.166452, 0.054436, -0.984546), (0.979906, -0.102156, -0.171316)141.95, -30.15, 234.9
88generate(0.495667, -0.399875, 0.770983), (0.19946, -0.811567, -0.549158), (0.845299, 0.42598, -0.322508)141.95, -30.15, 234.9
89generate(0.175564, -0.746234, -0.642115), (0.743081, 0.528289, -0.410781), (0.645761, -0.405025, 0.647262)141.95, -30.15, 234.9
90generate(0.743112, 0.59131, -0.313268), (0.567638, -0.309114, 0.763044), (0.35436, -0.74485, -0.565356)141.95, -30.15, 234.9
91generate(-0.999638, 0.025554, 0.008453), (-0.026384, -0.992435, -0.119901), (0.005325, -0.12008, 0.99275)141.95, -30.15, 234.9
92generate(-0.795055, 0.592708, -0.128782), (0.432232, 0.404701, -0.805849), (-0.425515, -0.696358, -0.577947)141.95, -30.15, 234.9
93generate(-0.795081, 0.397618, 0.45798), (0.564063, 0.207271, 0.799294), (0.222888, 0.893833, -0.389079)141.95, -30.15, 234.9
94generate(-0.979153, -0.011999, 0.202768), (0.012963, 0.992527, 0.121333), (-0.202708, 0.121433, -0.971681)141.95, -30.15, 234.9
95generate(-0.857562, 0.448863, -0.251215), (-0.443441, -0.397637, 0.803272), (0.260667, 0.800254, 0.540042)141.95, -30.15, 234.9
96generate(-0.727742, 0.569086, 0.382797), (-0.574392, -0.200715, -0.793592), (-0.374789, -0.797405, 0.472946)141.95, -30.15, 234.9
97generate(-0.504829, -0.291746, -0.812424), (-0.221678, -0.865777, 0.448653), (-0.83427, 0.40659, 0.372395)141.95, -30.15, 234.9
98generate(0.112604, 0.99172, 0.061738), (-0.044205, 0.067072, -0.996768), (-0.992656, 0.109511, 0.051392)141.95, -30.15, 234.9
99generate(-0.336627, -0.41407, 0.845712), (0.418185, 0.738962, 0.528258), (-0.843685, 0.53149, -0.075596)141.95, -30.15, 234.9
100generate(-0.317978, 0.297383, 0.900252), (-0.299633, 0.869348, -0.393007), (-0.899505, -0.394713, -0.187328)141.95, -30.15, 234.9
101generate(-0.799783, -0.558622, -0.219746), (-0.391175, 0.207329, 0.896659), (-0.455333, 0.803092, -0.384337)141.95, -30.15, 234.9
102generate(-0.296582, 0.816038, -0.496106), (-0.819371, -0.484284, -0.306756), (-0.490581, 0.315516, 0.812268)141.95, -30.15, 234.9
103generate(0.309623, -0.804371, -0.507072), (-0.739791, -0.538805, 0.402987), (-0.597364, 0.250353, -0.761892)141.95, -30.15, 234.9
104generate(0.806021, 0.428328, -0.408491), (-0.557132, 0.316029, -0.767939), (-0.199835, 0.846558, 0.493361)141.95, -30.15, 234.9
105generate(0.655502, -0.318718, 0.684643), (-0.191652, 0.806694, 0.55903), (-0.73047, -0.497659, 0.467706)141.95, -30.15, 234.9
106generate(0.420541, 0.799369, 0.429133), (-0.800814, 0.549359, -0.238539), (-0.426429, -0.24334, 0.871174)141.95, -30.15, 234.9
107generate(-0.196214, -0.812662, 0.548708), (-0.729528, 0.494895, 0.472089), (-0.655201, -0.307667, -0.689965)141.95, -30.15, 234.9
108generate(-0.093588, -0.037991, -0.994886), (-0.993954, -0.054058, 0.095565), (-0.057412, 0.997815, -0.032702)141.95, -30.15, 234.9
109generate(0.318172, -0.803889, 0.502523), (-0.864708, -0.463385, -0.193791), (0.388648, -0.372876, -0.842565)141.95, -30.15, 234.9
110generate(0.326918, -0.31888, -0.889629), (-0.3977, 0.807522, -0.435595), (0.857298, 0.496209, 0.137175)141.95, -30.15, 234.9
111generate(0.810217, 0.551902, 0.197366), (-0.422674, 0.316864, 0.849084), (0.406073, -0.771364, 0.490003)141.95, -30.15, 234.9
112generate(0.215796, 0.800231, -0.559519), (-0.797965, 0.474775, 0.371268), (0.562746, 0.366359, 0.741011)141.95, -30.15, 234.9
113generate(0.119034, 0.037817, 0.99217), (-0.990907, 0.067655, 0.116304), (-0.062727, -0.996992, 0.045526)141.95, -30.15, 234.9
114generate(-0.39929, -0.812762, -0.424246), (-0.856873, 0.495407, -0.142623), (0.326093, 0.306577, -0.894245)141.95, -30.15, 234.9
115generate(-0.490995, -0.290967, 0.821134), (-0.423798, -0.743744, -0.516953), (0.76113, -0.601817, 0.241863)141.95, -30.15, 234.9
116generate(-0.662602, -0.217288, -0.71676), (0.21376, 0.862324, -0.459025), (0.71782, -0.457365, -0.52493)141.95, -30.15, 234.9
117generate(-0.086292, 0.994622, 0.057281), (0.044384, -0.0536, 0.997576), (0.995281, 0.088626, -0.03952)141.95, -30.15, 234.9
118generate(-0.649263, 0.298778, -0.699421), (-0.295023, 0.748668, 0.593682), (0.701013, 0.591801, -0.397936)141.95, -30.15, 234.9
119generate(-0.289702, 0.817482, 0.497791), (-0.814095, -0.48396, 0.320986), (0.503311, -0.312259, 0.805712)141.95, -30.15, 234.9
120generate(-0.791218, -0.437568, 0.427209), (-0.597569, 0.404768, -0.692152), (0.129944, -0.80293, -0.581737)141.95, -30.15, 234.9

-
Components

#1: Protein COAT PROTEIN


Mass: 14568.501 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PRR1 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03616
#2: RNA chain 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3' / COAT PROTEIN-BINDING RNA HAIRPIN


Mass: 6406.879 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS PHAGE PRR1 (virus)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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

CrystalDescription: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 259990 / % possible obs: 16 % / Redundancy: 1.24 % / Rmerge(I) obs: 0.13
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 1.08 % / Rmerge(I) obs: 0.39 / % possible all: 15

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VF9

2vf9


Resolution: 3.5→29.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 595799.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
Details: BULK SOLVENT MODEL USED. ALTERNATE OCCUPANCY USED FOR TWO POSITIONS OF RNA CHAIN R RNA CHAIN S HAS ALTERNATE OCCUPANCY WITH RESPECT TO SYMMETRY-RELATED COPY OF ITSELF.
RfactorNum. reflection% reflectionSelection details
Rfree0.313 12256 5 %RANDOM
Rwork0.308 ---
obs0.308 243543 15.1 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.6 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.86 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 534 1 0 3607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 3.5→3.56 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 553 4.8 %
Rwork0.404 10909 -
obs--14.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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