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- PDB-2vf9: Crystal structure of bacteriophage PRR1 -

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Basic information

Entry
Database: PDB / ID: 2vf9
TitleCrystal structure of bacteriophage PRR1
ComponentsCOAT PROTEIN
KeywordsVIRUS / VIRION / RNA-BINDING / CAPSID PROTEIN / STRUCTURAL PROTEIN
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
Biological speciesBACTERIOPHAGE PRR1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPersson, M. / Tars, K. / Liljas, L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Capsid of the Small RNA Phage Prr1 is Stabilized by Metal Ions
Authors: Persson, M. / Tars, K. / Liljas, L.
History
DepositionNov 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Other / Version format compliance
Revision 1.2Dec 13, 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
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_asym_id / _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_asym_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7464
Polymers43,7063
Non-polymers401
Water0
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)2,624,735240
Polymers2,622,330180
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
hetero molecules
x 5


  • icosahedral pentamer
  • 219 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)218,72820
Polymers218,52815
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 262 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)262,47324
Polymers262,23318
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
hetero molecules
x 60
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 5.25 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)5,249,470480
Polymers5,244,660360
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)281.400, 285.400, 472.500
Angle α, β, γ (deg.)93.27, 90.00, 119.44
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(0.315514, 0.864434, -0.391414), (-0.801019, 0.463767, 0.378535), (0.508743, 0.194097, 0.838753)
3generate(0.315514, -0.801019, 0.508743), (0.864434, 0.463767, 0.194097), (-0.391414, 0.378535, 0.838753)
4generate(-0.401316, 0.856449, -0.324717), (-0.815064, -0.495661, -0.299985), (-0.417871, 0.144276, 0.896977)
5generate(-0.19203, -0.810647, 0.553151), (0.729967, -0.494716, -0.471597), (0.655952, 0.313221, 0.686746)
6generate(-0.792008, 0.597665, -0.124578), (-0.431642, -0.403876, 0.806579), (0.43175, 0.69259, 0.57785)
7generate(-0.667629, -0.214717, -0.712859), (-0.214717, -0.86129, 0.460518), (-0.712859, 0.460518, 0.528919)
8generate(-0.792008, -0.431642, 0.43175), (0.597665, -0.403876, 0.69259), (-0.124578, 0.806579, 0.57785)
9generate(-0.311595, 0.299856, 0.901663), (0.299856, -0.869389, 0.392746), (0.901663, 0.392746, 0.180984)
10generate(0.740821, 0.595738, -0.31029), (-0.568212, 0.309456, -0.762478), (-0.358216, 0.74117, 0.567757)
11generate(0.489246, -0.200081, -0.848885), (-0.402075, 0.811979, -0.423114), (0.773934, 0.548322, 0.316809)
12generate(0.870167, -0.434584, 0.232262), (0.38667, 0.31004, -0.86854), (0.305443, 0.845584, 0.437827)
13generate(0.506648, 0.317149, 0.801701), (0.307345, 0.802351, -0.511637), (-0.80551, 0.505619, 0.309035)
14generate(0.120212, 0.990813, 0.061964), (0.04472, -0.067758, 0.996699), (0.99174, -0.117044, -0.052454)
15generate(-0.117232, 0.165363, -0.97924), (-0.992527, -0.053123, 0.109852), (-0.033855, 0.984801, 0.170355)
16generate(0.321462, -0.323648, -0.889896), (0.395712, -0.807869, 0.436761), (-0.860276, -0.492545, -0.131627)
17generate(0.120212, 0.04472, 0.99174), (0.990813, -0.067758, -0.117044), (0.061964, 0.996699, -0.052454)
18generate(0.660094, 0.191061, 0.726479), (-0.316502, -0.806339, 0.499643), (0.681251, -0.559744, -0.471788)
19generate(-0.092054, 0.99417, 0.056144), (-0.044941, 0.052178, -0.997626), (-0.994739, -0.094359, 0.039876)
20generate(-0.499112, -0.293493, -0.815321), (0.223874, 0.865278, -0.448524), (0.837118, -0.406393, -0.366166)
21generate(-0.499113, 0.223874, 0.837118), (-0.293493, 0.865278, -0.406393), (-0.815321, -0.448524, -0.366166)
22generate(0.780216, -0.607676, 0.148298), (-0.399623, -0.30186, 0.865553), (-0.481211, -0.734582, -0.478357)
23generate(0.808374, 0.42141, -0.411029), (0.556053, -0.317439, 0.768139), (0.193225, -0.849498, -0.490936)
24generate(-0.291612, 0.814443, -0.501642), (0.820502, 0.482547, 0.306471), (0.491669, -0.322228, -0.808969)
25generate(-0.337173, -0.850653, 0.403367), (-0.725814, 0.507755, 0.46409), (-0.599591, -0.136291, -0.788616)
26generate(-0.757188, -0.585506, 0.289569), (-0.585506, 0.411859, -0.698252), (0.289569, -0.698252, -0.654672)
27generate(-0.858375, 0.444595, -0.255982), (0.444595, 0.395696, -0.803592), (-0.255982, -0.803592, -0.53732)
28generate(0.213689, 0.796866, -0.565104), (0.796866, -0.476806, -0.371027), (-0.565104, -0.371027, -0.736883)
29generate(0.377414, -0.869873, 0.317616), (-0.869873, -0.450653, -0.200583), (0.317616, -0.200583, -0.926761)
30generate(-0.999599, 0.028265, 0.001682), (0.028265, 0.992545, 0.118558), (0.001682, 0.118558, -0.992946)
31generate(-0.97785, -0.012745, 0.208919), (-0.012745, -0.992667, -0.120211), (0.208919, -0.120211, 0.970516)
32generate(-0.401316, -0.815064, -0.417871), (0.856449, -0.495661, 0.144276), (-0.324717, -0.299985, 0.896977)
33generate(-0.19203, 0.729967, 0.655952), (-0.810647, -0.494716, 0.313221), (0.553151, -0.471597, 0.686746)
34generate(0.313672, -0.806019, -0.50194), (0.740655, 0.538476, -0.401839), (0.594172, -0.245719, 0.765886)
35generate(0.313672, 0.740655, 0.594172), (-0.806019, 0.538476, -0.245719), (-0.50194, -0.401839, 0.765886)
36generate(0.740821, -0.568212, -0.358216), (0.595738, 0.309456, 0.74117), (-0.31029, -0.762478, 0.567757)
37generate(0.506648, 0.307345, -0.80551), (0.317149, 0.802351, 0.505619), (0.801701, -0.511637, 0.309035)
38generate(0.870167, 0.38667, 0.305443), (-0.434584, 0.31004, 0.845584), (0.232262, -0.86854, 0.437827)
39generate(0.489246, -0.402075, 0.773934), (-0.200081, 0.811979, 0.548322), (-0.848885, -0.423114, 0.316809)
40generate(-0.79683, -0.563511, -0.217984), (0.392386, -0.208286, -0.895907), (0.45945, -0.79942, 0.387082)
41generate(-0.653207, 0.294424, -0.697593), (0.294424, -0.750037, -0.592249), (-0.697593, -0.592249, 0.403244)
42generate(-0.79683, 0.392386, 0.45945), (-0.563511, -0.208286, -0.79942), (-0.217984, -0.895907, 0.387083)
43generate(-0.331978, -0.417654, 0.845787), (-0.417654, -0.738879, -0.528794), (0.845787, -0.528794, 0.070857)
44generate(-0.117232, -0.992527, -0.033855), (0.165363, -0.053123, 0.984801), (-0.97924, 0.109852, 0.170355)
45generate(-0.092054, -0.044941, -0.994739), (0.99417, 0.052178, -0.094359), (0.056144, -0.997626, 0.039876)
46generate(-0.496132, 0.424153, -0.757593), (-0.285403, 0.744397, 0.60367), (0.819999, 0.51572, -0.248265)
47generate(0.089074, -0.165142, 0.982239), (-0.992455, 0.068703, 0.101551), (-0.084253, -0.983874, -0.157777)
48generate(-0.496132, -0.285403, 0.819999), (0.424153, 0.744397, 0.51572), (-0.757593, 0.60367, -0.248265)
49generate(0.089074, -0.992455, -0.084253), (-0.165142, 0.068703, -0.983874), (0.982239, 0.101551, -0.157777)
50generate(0.321462, 0.395712, -0.860276), (-0.323648, -0.807869, -0.492545), (-0.889896, 0.436761, -0.131627)
51generate(0.660094, -0.316502, 0.681251), (0.191061, -0.806339, -0.559744), (0.726479, 0.499643, -0.471788)
52generate(-0.724208, 0.575449, 0.379977), (0.575449, 0.20069, 0.792832), (0.379977, 0.792832, -0.476482)
53generate(-0.881711, -0.379212, -0.280684), (-0.379212, 0.215685, 0.899821), (-0.280684, 0.899821, -0.333974)
54generate(0.16997, -0.744451, -0.64568), (-0.744451, -0.526307, 0.410846), (-0.64568, 0.410846, -0.643663)
55generate(0.424817, 0.800223, 0.42329), (0.800223, -0.550569, 0.237733), (0.42329, 0.237733, -0.874247)
56generate(0.808374, 0.556053, 0.193225), (0.42141, -0.317439, -0.849498), (-0.411029, 0.768139, -0.490936)
57generate(0.780216, -0.399623, -0.481211), (-0.607676, -0.30186, -0.734582), (0.148298, 0.865553, -0.478357)
58generate(-0.337173, -0.725814, -0.599591), (-0.850653, 0.507755, -0.136291), (0.403367, 0.46409, -0.788616)
59generate(-0.291612, 0.820502, 0.491669), (0.814443, 0.482547, -0.322228), (-0.501642, 0.306471, -0.808969)
60generate(0.977449, -0.01552, -0.210601), (-0.01552, -0.999878, 0.001653), (-0.210601, 0.001653, -0.977571)
61generate(0.978692, -0.013168, -0.204912), (0.013215, 0.999912, -0.001136), (0.204908, -0.001596, 0.97878)142.2, -30.04999, -214.74836
62generate(0.215091, 0.800135, -0.559929), (-0.797357, 0.474929, 0.372376), (0.563877, 0.366368, 0.740147)142.2, -30.04999, -214.74836
63generate(0.377613, -0.867624, 0.323476), (0.868972, 0.452711, 0.19985), (-0.319836, 0.205627, 0.924891)142.2, -30.04999, -214.74836
64generate(-0.296405, 0.815162, -0.497649), (-0.819821, -0.484463, -0.305269), (-0.489936, 0.317499, 0.811885)142.2, -30.04999, -214.74836
65generate(-0.331963, -0.851042, 0.406852), (0.72662, -0.505741, -0.465026), (0.601519, 0.141256, 0.786271)142.2, -30.04999, -214.74836
66generate(-0.857919, 0.448328, -0.250953), (-0.442561, -0.396729, 0.804205), (0.260988, 0.801004, 0.538774)142.2, -30.04999, -214.74836
67generate(-0.504503, -0.293166, -0.812115), (-0.222711, -0.864574, 0.450456), (-0.834192, 0.408123, 0.37089)142.2, -30.04999, -214.74836
68generate(-0.757475, -0.582404, 0.295022), (0.587287, -0.410461, 0.697578), (-0.285177, 0.701661, 0.652952)142.2, -30.04999, -214.74836
69generate(-0.493665, 0.224436, 0.840192), (0.294687, -0.865796, 0.404422), (0.818202, 0.447243, 0.361274)142.2, -30.04999, -214.74836
70generate(0.805921, 0.427094, -0.409978), (-0.557965, 0.316459, -0.767156), (-0.197907, 0.84702, 0.493345)142.2, -30.04999, -214.74836
71generate(0.325527, -0.318868, -0.890144), (-0.396454, 0.808641, -0.434655), (0.858404, 0.494393, 0.136819)142.2, -30.04999, -214.74836
72generate(0.783945, -0.602677, 0.149034), (0.397788, 0.303309, -0.865892), (0.476649, 0.738096, 0.477515)142.2, -30.04999, -214.74836
73generate(0.656864, 0.196218, 0.72803), (0.314928, 0.805897, -0.501349), (-0.685092, 0.558595, 0.467569)142.2, -30.04999, -214.74836
74generate(-0.086158, 0.994576, 0.058267), (0.045178, -0.054525, 0.99749), (0.995257, 0.088573, -0.040235)142.2, -30.04999, -214.74836
75generate(-0.094727, -0.039258, -0.994729), (-0.993951, -0.052052, 0.096708), (-0.055574, 0.997873, -0.034089)142.2, -30.04999, -214.74836
76generate(0.485682, -0.205186, -0.849713), (0.400903, -0.811515, 0.425112), (-0.776782, -0.547122, -0.311878)142.2, -30.04999, -214.74836
77generate(0.091906, -0.159576, 0.982898), (0.992244, -0.068293, -0.103868), (0.0837, 0.984821, 0.152061)142.2, -30.04999, -214.74836
78generate(0.5106, 0.312306, 0.801095), (-0.308525, -0.803108, 0.509736), (0.802558, -0.507429, -0.313713)142.2, -30.04999, -214.74836
79generate(0.114333, 0.991634, 0.059914), (-0.045024, 0.065419, -0.996842), (-0.992422, 0.111274, 0.052126)142.2, -30.04999, -214.74836
80generate(-0.662961, -0.215358, -0.71701), (0.216308, 0.861785, -0.458843), (0.716725, -0.45929, -0.524746)142.2, -30.04999, -214.74836
81generate(-0.317544, 0.299618, 0.899664), (-0.299136, 0.86867, -0.394879), (-0.899824, -0.394514, -0.186215)142.2, -30.04999, -214.74836
82generate(0.86746, -0.440228, 0.231761), (-0.38873, -0.309029, 0.86798), (-0.310489, -0.84303, -0.4392)142.2, -30.04999, -214.74836
83generate(0.744233, 0.590683, -0.311787), (0.566467, -0.310877, 0.763197), (0.353879, -0.744615, -0.565967)142.2, -30.04999, -214.74836
84generate(-0.396952, 0.856763, -0.329221), (0.816018, 0.493633, 0.300733), (0.420173, -0.149275, -0.895082)142.2, -30.04999, -214.74836
85generate(-0.197567, -0.811285, 0.550258), (-0.729524, 0.496624, 0.470276), (-0.654799, -0.308514, -0.689969)142.2, -30.04999, -214.74836
86generate(-0.79268, -0.435373, 0.426743), (-0.595789, 0.404879, -0.69362), (0.129205, -0.804067, -0.58033)142.2, -30.04999, -214.74836
87generate(-0.793486, 0.594577, -0.129843), (0.433503, 0.402449, -0.806294), (-0.427148, -0.69607, -0.577089)142.2, -30.04999, -214.74836
88generate(0.314439, 0.862192, -0.397181), (0.800261, -0.465812, -0.377625), (-0.510598, -0.199109, -0.836448)142.2, -30.04999, -214.74836
89generate(0.315744, -0.804301, 0.503394), (-0.865169, -0.461881, -0.195315), (0.3896, -0.373851, -0.841693)142.2, -30.04999, -214.74836
90generate(-0.979016, -0.009701, 0.203551), (0.015051, 0.992696, 0.119698), (-0.203225, 0.12025, -0.97172)142.2, -30.04999, -214.74836
91generate(-0.999656, 0.025231, 0.00718), (-0.025904, -0.992611, -0.118542), (0.004137, -0.118687, 0.992923)142.2, -30.04999, -214.74836
92generate(-0.337504, -0.729699, -0.594668), (0.851439, -0.506048, 0.137722), (-0.401426, -0.459841, 0.792088)142.2, -30.04999, -214.74836
93generate(-0.290611, 0.817563, 0.497128), (-0.813742, -0.48449, 0.321082), (0.503358, -0.311225, 0.806083)142.2, -30.04999, -214.74836
94generate(0.175482, -0.745584, -0.642893), (0.74406, 0.528056, -0.409306), (0.644655, -0.406524, 0.647424)142.2, -30.04999, -214.74836
95generate(0.420455, 0.800124, 0.427808), (-0.801232, 0.548673, -0.238715), (-0.425729, -0.242405, 0.871777)142.2, -30.04999, -214.74836
96generate(0.780773, -0.403939, -0.476683), (0.605828, 0.302786, 0.735726), (-0.152856, -0.863223, 0.481125)142.2, -30.04999, -214.74836
97generate(0.327398, 0.395071, -0.85833), (0.322906, 0.806923, 0.494578), (0.887999, -0.439084, 0.136615)142.2, -30.04999, -214.74836
98generate(0.809755, 0.552322, 0.198084), (-0.42331, 0.316109, 0.849049), (0.406331, -0.771373, 0.489774)142.2, -30.04999, -214.74836
99generate(0.655402, -0.317499, 0.685305), (-0.192634, 0.807075, 0.558142), (-0.730302, -0.49782, 0.467797)142.2, -30.04999, -214.74836
100generate(-0.879165, -0.38495, -0.28086), (0.3813, -0.214806, -0.899149), (0.285798, -0.897592, 0.335632)142.2, -30.04999, -214.74836
101generate(-0.50022, 0.419386, -0.757559), (0.286558, -0.745407, -0.601874), (-0.817107, -0.518155, 0.25269)142.2, -30.04999, -214.74836
102generate(-0.727764, 0.57035, 0.380869), (-0.573744, -0.202065, -0.793718), (-0.375736, -0.796161, 0.47429)142.2, -30.04999, -214.74836
103generate(-0.492716, -0.290669, 0.820209), (-0.422965, -0.743733, -0.517651), (0.760482, -0.601974, 0.243506)142.2, -30.04999, -214.74836
104generate(0.083747, -0.993189, -0.08101), (0.164912, -0.06636, 0.984073), (-0.982747, -0.095771, 0.158231)142.2, -30.04999, -214.74836
105generate(-0.114688, 0.159755, -0.980472), (0.992802, 0.052713, -0.107541), (0.034504, -0.985748, -0.16465)142.2, -30.04999, -214.74836
106generate(-0.64983, 0.299636, -0.698527), (-0.292866, 0.749351, 0.593888), (0.701392, 0.590501, -0.399197)142.2, -30.04999, -214.74836
107generate(0.117509, 0.039079, 0.992303), (-0.991095, 0.067632, 0.114702), (-0.062629, -0.996945, 0.046678)142.2, -30.04999, -214.74836
108generate(-0.335906, -0.412823, 0.846607), (0.41842, 0.739874, 0.526793), (-0.843855, 0.531191, -0.075795)142.2, -30.04999, -214.74836
109generate(-0.111922, -0.993022, -0.037172), (-0.165066, 0.055466, -0.984722), (0.979912, -0.104075, -0.170123)142.2, -30.04999, -214.74836
110generate(0.501224, 0.308421, -0.808487), (-0.318361, -0.803064, -0.50372), (-0.804625, 0.509867, -0.304325)142.2, -30.04999, -214.74836
111generate(0.494648, -0.401523, 0.770781), (0.198942, -0.811018, -0.550156), (0.846017, 0.425474, -0.32129)142.2, -30.04999, -214.74836
112generate(-0.794215, 0.398084, 0.459077), (0.565396, 0.207376, 0.798325), (0.222599, 0.893602, -0.389777)142.2, -30.04999, -214.74836
113generate(-0.800415, -0.558356, -0.218116), (-0.390512, 0.209633, 0.896412), (-0.454792, 0.802679, -0.385837)142.2, -30.04999, -214.74836
114generate(0.308459, -0.805845, -0.505438), (-0.741406, -0.536565, 0.403008), (-0.595963, 0.250424, -0.762966)142.2, -30.04999, -214.74836
115generate(0.31849, 0.741707, 0.590284), (0.805285, -0.540216, 0.244299), (0.500079, 0.397539, -0.76934)142.2, -30.04999, -214.74836
116generate(0.869825, 0.390984, 0.300892), (0.432522, -0.310935, -0.846312), (-0.237337, 0.866286, -0.439569)142.2, -30.04999, -214.74836
117generate(0.741206, -0.564495, -0.363263), (-0.59748, -0.308097, -0.740333), (0.305993, 0.765782, -0.565638)142.2, -30.04999, -214.74836
118generate(-0.401441, -0.812132, -0.423423), (-0.855492, 0.497591, -0.143306), (0.327076, 0.304707, -0.894525)142.2, -30.04999, -214.74836
119generate(-0.19333, 0.733865, 0.651203), (0.811088, 0.492999, -0.314783), (-0.552051, 0.467325, -0.690541)142.2, -30.04999, -214.74836
120generate(0.99998, -0.002362, -0.005819), (-0.002363, -0.999997, -2.0E-5), (-0.00582, 3.3E-5, -0.999983)142.2, -30.04999, -214.74836

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Components

#1: Protein COAT PROTEIN / PRR1 COAT PROTEIN


Mass: 14568.501 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE PRR1 (virus) / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03616
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Sequence detailsTHERE IS AN ERROR IN THE SEQUENCE IN THE UNIPROT ENTRY.

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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: Nov 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 1617870 / % possible obs: 63 % / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 4.6
Reflection shellResolution: 3.48→3.55 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.2 / % possible all: 66

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Processing

Software
NameClassification
CNSmodel building
PHASERmodel building
DENZOdata reduction
DENZOphasing
SCALEPACKphasing
GLRFphasing
CNSphasing
MOLEMAN2phasing
AVEphasing
Ophasing
PHASERphasing
MAMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 3.5→29.12 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 299537.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.313 50827 5 %RANDOM
Rwork0.311 ---
obs0.311 1617870 63 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.207761 e/Å3
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å2-3.12 Å2-0.41 Å2
2---11.17 Å22.61 Å2
3---14.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.62 Å
Luzzati d res low-5 Å
Luzzati sigma a0.98 Å0.96 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 1 0 3073
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
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
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 8718 5 %
Rwork0.388 166186 -
obs--65.2 %
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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