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- PDB-1dwn: Structure of bacteriophage PP7 from Pseudomonas aeruginosa at 3.7... -

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Basic information

Entry
Database: PDB / ID: 1dwn
TitleStructure of bacteriophage PP7 from Pseudomonas aeruginosa at 3.7 A resolution
ComponentsPHAGE COAT PROTEIN
KeywordsVIRUS / PHAGE / BACTERIOPHAGE / COAT PROTEIN / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


T=3 icosahedral viral capsid / regulation of translation / RNA binding / identical protein binding
Similarity search - Function
Bacteriophage PP7, coat / Phage PP7 coat protein / MS2 Viral Coat Protein / MS2 Viral Coat Protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACTERIOPHAGE PP7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTars, K. / Fridborg, K. / Bundule, M. / Liljas, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure Determination of Phage Pp7 from Pseudomonas Aeruginosa: From Poor Data to a Good Map
Authors: Tars, K. / Fridborg, K. / Bundule, M. / Liljas, L.
History
DepositionDec 9, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Other / Refinement description / Version format compliance
Revision 1.2Dec 6, 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_sheet
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_sheet.number_strands
Revision 1.3Feb 19, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHAGE COAT PROTEIN
B: PHAGE COAT PROTEIN
C: PHAGE COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,7203
Polymers41,7203
Non-polymers00
Water00
1
A: PHAGE COAT PROTEIN
B: PHAGE COAT PROTEIN
C: PHAGE COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)2,503,226180
Polymers2,503,226180
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: PHAGE COAT PROTEIN
B: PHAGE COAT PROTEIN
C: PHAGE COAT PROTEIN
x 5


  • icosahedral pentamer
  • 209 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)208,60215
Polymers208,60215
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: PHAGE COAT PROTEIN
B: PHAGE COAT PROTEIN
C: PHAGE COAT PROTEIN
x 6


  • icosahedral 23 hexamer
  • 250 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)250,32318
Polymers250,32318
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: PHAGE COAT PROTEIN
B: PHAGE COAT PROTEIN
C: PHAGE COAT PROTEIN
x 60
A: PHAGE COAT PROTEIN
B: PHAGE COAT PROTEIN
C: PHAGE COAT PROTEIN
x 60


  • crystal asymmetric unit, crystal frame
  • 5.01 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)5,006,452360
Polymers5,006,452360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation118
transform to crystal frame1
Unit cell
Length a, b, c (Å)285.000, 324.000, 380.000
Angle α, β, γ (deg.)88.40, 88.10, 87.70
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(0.298065, -0.901822, -0.312848), (-0.511568, 0.125786, -0.849986), (0.805888, 0.413394, -0.423851)
3generate(0.298065, -0.511568, 0.805888), (-0.901822, 0.125786, 0.413394), (-0.312848, -0.849986, -0.423851)
4generate(-0.567623, -0.814264, 0.121564), (-0.814264, 0.533445, -0.228933), (0.121564, -0.228933, -0.965822)
5generate(0.34533, 0.459727, 0.818168), (-0.700092, 0.706781, -0.101646), (-0.624995, -0.537691, 0.565923)
6generate(0.527101, 0.084627, -0.845578), (-0.652155, 0.678241, -0.338649), (0.544847, 0.72995, 0.412692)
7generate(0.454573, 0.10749, 0.8842), (0.444703, 0.832726, -0.329858), (-0.771753, 0.543151, 0.330734)
8generate(0.79307, -0.0309, -0.608346), (-0.559274, -0.432659, -0.70712), (-0.241356, 0.901028, -0.360411)
9generate(-0.238065, -0.970582, 0.036002), (-0.515225, 0.157624, 0.842436), (-0.823327, 0.182005, -0.537593)
10generate(-0.238065, -0.515225, -0.823327), (-0.970582, 0.157624, 0.182005), (0.036002, 0.842436, -0.537593)
11generate(-0.470896, -0.190475, 0.86138), (-0.223256, 0.970359, 0.092524), (-0.853472, -0.148739, -0.499463)
12generate(0.651259, 0.756795, -0.055877), (-0.488385, 0.361643, -0.794162), (-0.580811, 0.544495, 0.605131)
13generate(-0.427945, 0.618626, 0.658912), (0.827034, 0.562072, 0.00943), (-0.364523, 0.548978, -0.752161)
14generate(0.086985, 0.736135, -0.671222), (-0.033429, -0.671239, -0.740487), (-0.995649, 0.086849, -0.03378)
15generate(-0.891585, -0.263329, -0.36842), (-0.263329, -0.360399, 0.894858), (-0.36842, 0.894858, 0.251984)
16generate(-0.180713, 0.527617, -0.830038), (-0.925973, -0.375748, -0.037247), (-0.331538, 0.761862, 0.556461)
17generate(-0.992694, -0.113796, -0.040119), (-0.113796, 0.772401, 0.624857), (-0.040119, 0.624857, -0.779708)
18generate(-0.270004, 0.864334, 0.424292), (0.07451, 0.458093, -0.885776), (-0.959972, -0.207549, -0.188089)
19generate(-0.427945, 0.827034, -0.364523), (0.618626, 0.562072, 0.548978), (0.658912, 0.00943, -0.752161)
20generate(-0.844404, 0.339268, -0.414583), (0.339268, -0.260245, -0.903974), (-0.414583, -0.903974, 0.104649)
21generate(-0.759353, 0.632791, 0.151519), (-0.494245, -0.712392, 0.498215), (0.423207, 0.303434, 0.853712)
22generate(-0.474825, 0.873089, 0.110706), (-0.742085, -0.329569, -0.58369), (-0.473128, -0.359304, 0.804395)
23generate(-0.498957, 0.583795, -0.640488), (-0.522981, 0.38648, 0.759687), (0.691037, 0.714014, 0.112477)
24generate(-0.963534, 0.258629, -0.068649), (0.258629, 0.8343, -0.486882), (-0.068649, -0.486882, -0.870766)
25generate(0.454573, 0.444703, -0.771753), (0.10749, 0.832726, 0.543151), (0.8842, -0.329858, 0.330734)
26generate(-0.713949, -0.673045, -0.193096), (0.043762, 0.232343, -0.971649), (0.698828, -0.702158, -0.136428)
27generate(-0.024109, 0.479371, 0.877281), (-0.888856, -0.411914, 0.200655), (0.457552, -0.774939, 0.436023)
28generate(-0.713949, 0.043762, 0.698828), (-0.673045, 0.232343, -0.702158), (-0.193096, -0.971649, -0.136428)
29generate(0.327987, 0.938252, -0.110038), (-0.885332, 0.345924, 0.310683), (0.329563, -0.00448, 0.944123)
30generate(-0.470896, -0.223256, -0.853472), (-0.190475, 0.970359, -0.148739), (0.86138, 0.092524, -0.499463)
31generate(-0.799937, 0.01668, -0.599852), (0.01668, -0.998609, -0.050012), (-0.599852, -0.050012, 0.798547)
32generate(-0.73038, 0.475524, 0.490329), (0.475524, -0.161328, 0.864783), (0.490329, 0.864783, -0.108293)
33generate(-0.065813, 0.921186, -0.383517), (0.921186, -0.091634, -0.37818), (-0.383517, -0.37818, -0.842553)
34generate(0.367561, 0.797584, 0.478287), (0.797584, -0.534836, 0.278945), (0.478287, 0.278945, -0.832725)
35generate(0.086985, -0.033429, -0.995649), (0.736135, -0.671239, 0.086849), (-0.671222, -0.740487, -0.03378)
36generate(-0.759353, -0.494245, 0.423207), (0.632791, -0.712392, 0.303434), (0.151519, 0.498215, 0.853711)
37generate(0.106724, -0.397905, -0.911198), (-0.397905, -0.85694, 0.327607), (-0.911198, 0.327607, -0.249785)
38generate(-0.498957, -0.522981, 0.691037), (0.583795, 0.38648, 0.714014), (-0.640488, 0.759687, 0.112477)
39generate(0.675717, 0.669858, 0.307728), (0.551714, -0.182696, -0.813778), (-0.488894, 0.719661, -0.493021)
40generate(0.152652, -0.090559, 0.984122), (0.963461, -0.20813, -0.168599), (0.220094, 0.9739, 0.055479)
41generate(0.88492, 0.257775, -0.387904), (0.257775, -0.964748, -0.053048), (-0.387904, -0.053048, -0.920172)
42generate(-0.180713, -0.925973, -0.331538), (0.527617, -0.375748, 0.761862), (-0.830038, -0.037247, 0.556461)
43generate(0.574784, -0.814792, -0.075746), (-0.814792, -0.578427, 0.039191), (-0.075746, 0.039191, -0.996357)
44generate(0.527101, -0.652155, 0.544847), (0.084627, 0.678241, 0.72995), (-0.845578, -0.338649, 0.412692)
45generate(0.929818, -0.332147, 0.158486), (0.266517, 0.310752, -0.912361), (0.253788, 0.890569, 0.377465)
46generate(0.327987, -0.885332, 0.329563), (0.938252, 0.345924, -0.00448), (-0.110038, 0.310683, 0.944123)
47generate(0.81626, -0.270908, 0.510224), (0.099086, -0.804476, -0.585663), (0.569124, 0.528609, -0.629818)
48generate(0.79307, -0.559274, -0.241356), (-0.0309, -0.432659, 0.901028), (-0.608346, -0.70712, -0.360411)
49generate(-0.042601, -0.657857, 0.751937), (-0.657857, -0.547967, -0.516678), (0.751937, -0.516678, -0.409431)
50generate(0.929818, 0.266517, 0.253788), (-0.332147, 0.310752, 0.890568), (0.158486, -0.912361, 0.377465)
51generate(0.34533, -0.700092, -0.624995), (0.459727, 0.706781, -0.537691), (0.818168, -0.101646, 0.565923)
52generate(0.651259, -0.488385, -0.580811), (0.756795, 0.361643, 0.544495), (-0.055877, -0.794162, 0.605131)
53generate(-0.024109, -0.888856, 0.457552), (0.479371, -0.411914, -0.774939), (0.877281, 0.200655, 0.436023)
54generate(0.81626, 0.099086, 0.569123), (-0.270908, -0.804476, 0.528609), (0.510224, -0.585663, -0.629818)
55generate(-0.892226, -0.143979, 0.428022), (-0.143979, -0.807654, -0.571809), (0.428022, -0.571809, 0.69988)
56generate(0.152652, 0.963461, 0.220094), (-0.090559, -0.20813, 0.9739), (0.984122, -0.168599, 0.055479)
57generate(-0.270004, 0.07451, -0.959972), (0.864334, 0.458093, -0.207549), (0.424292, -0.885776, -0.188089)
58generate(0.675717, 0.551714, -0.488894), (0.669858, -0.182696, 0.719661), (0.307728, -0.813777, -0.493021)
59generate(-0.474825, -0.742085, -0.473128), (0.873089, -0.329569, -0.359304), (0.110706, -0.58369, 0.804395)
60generate(-0.14319, 0.139276, 0.979846), (0.139276, -0.97736, 0.159276), (0.979846, 0.159276, 0.120551)
61generate(0.999848, 1.0E-6, -0.01745), (3.0E-6, 1, 0.000274), (0.01745, -0.000274, 0.999848)154.561, 165.893, 188.853
62generate(0.308221, -0.912387, -0.269352), (-0.48875, 0.091039, -0.867661), (0.816164, 0.399077, -0.417869)154.561, 165.893, 188.853
63generate(0.327191, -0.47376, 0.817617), (-0.905358, 0.090689, 0.414852), (-0.270689, -0.875972, -0.39925)154.561, 165.893, 188.853
64generate(-0.535387, -0.830437, 0.154065), (-0.834814, 0.492603, -0.245822), (0.128246, -0.260225, -0.956993)154.561, 165.893, 188.853
65generate(0.358319, 0.473098, 0.804852), (-0.709271, 0.698528, -0.094833), (-0.607077, -0.536877, 0.58585)154.561, 165.893, 188.853
66generate(0.536549, 0.052621, -0.842227), (-0.647106, 0.666255, -0.370618), (0.541636, 0.743865, 0.39153)154.561, 165.893, 188.853
67generate(0.453465, 0.083094, 0.887392), (0.437805, 0.846479, -0.302985), (-0.776335, 0.525897, 0.34747)154.561, 165.893, 188.853
68generate(0.824828, -0.034724, -0.564316), (-0.518329, -0.445095, -0.730223), (-0.225818, 0.89481, -0.385126)154.561, 165.893, 188.853
69generate(-0.174478, -0.984031, 0.035229), (-0.541342, 0.125747, 0.831346), (-0.8225, 0.125981, -0.554637)154.561, 165.893, 188.853
70generate(-0.189224, -0.555544, -0.80967), (-0.981676, 0.125938, 0.143013), (0.022518, 0.821895, -0.569194)154.561, 165.893, 188.853
71generate(-0.445621, -0.215196, 0.868972), (-0.262171, 0.959491, 0.103167), (-0.855972, -0.181846, -0.483988)154.561, 165.893, 188.853
72generate(0.665876, 0.744437, -0.04923), (-0.470074, 0.367395, -0.802528), (-0.579345, 0.557526, 0.594579)154.561, 165.893, 188.853
73generate(-0.459872, 0.577688, 0.674385), (0.800885, 0.597852, 0.034005), (-0.383538, 0.555743, -0.737596)154.561, 165.893, 188.853
74generate(0.115864, 0.748687, -0.65272), (-0.006555, -0.656555, -0.75425), (-0.993243, 0.091669, -0.071163)154.561, 165.893, 188.853
75generate(-0.857779, -0.307667, -0.411772), (-0.292415, -0.36675, 0.883169), (-0.422739, 0.877972, 0.224625)154.561, 165.893, 188.853
76generate(-0.144518, 0.502934, -0.852158), (-0.921374, -0.382422, -0.069445), (-0.36081, 0.77512, 0.518657)154.561, 165.893, 188.853
77generate(-0.983212, -0.177053, -0.04411), (-0.166357, 0.770515, 0.615331), (-0.074959, 0.61234, -0.787033)154.561, 165.893, 188.853
78generate(-0.26618, 0.855683, 0.443797), (0.068345, 0.476001, -0.876785), (-0.961497, -0.203051, -0.185184)154.561, 165.893, 188.853
79generate(-0.477962, 0.800271, -0.362103), (0.587479, 0.597713, 0.545534), (0.653009, 0.048016, -0.755826)154.561, 165.893, 188.853
80generate(-0.838908, 0.355199, -0.412392), (0.339316, -0.25111, -0.906537), (-0.425557, -0.900432, 0.090133)154.561, 165.893, 188.853
81generate(-0.778414, 0.62062, 0.094355), (-0.502586, -0.706189, 0.498703), (0.376137, 0.340776, 0.861622)154.561, 165.893, 188.853
82generate(-0.46305, 0.882216, 0.085318), (-0.737244, -0.32994, -0.589585), (-0.491992, -0.335908, 0.803187)154.561, 165.893, 188.853
83generate(-0.511522, 0.534814, -0.672547), (-0.554241, 0.392758, 0.733866), (0.65663, 0.748141, 0.095512)154.561, 165.893, 188.853
84generate(-0.971549, 0.232621, -0.044494), (0.224074, 0.841985, -0.490768), (-0.0767, -0.486775, -0.870154)154.561, 165.893, 188.853
85generate(0.424195, 0.443242, -0.789681), (0.092507, 0.846254, 0.524688), (0.900834, -0.295621, 0.317973)154.561, 165.893, 188.853
86generate(-0.720025, -0.671401, -0.175458), (0.041303, 0.210929, -0.976628), (0.692718, -0.710443, -0.124143)154.561, 165.893, 188.853
87generate(-0.046062, 0.517968, 0.854159), (-0.881406, -0.423476, 0.209267), (0.470109, -0.743221, 0.476046)154.561, 165.893, 188.853
88generate(-0.704621, 0.058148, 0.707198), (-0.683746, 0.210855, -0.698592), (-0.189738, -0.975786, -0.108815)154.561, 165.893, 188.853
89generate(0.31759, 0.936629, -0.147859), (-0.88978, 0.348268, 0.29496), (0.327762, 0.037886, 0.944)154.561, 165.893, 188.853
90generate(-0.475435, -0.263698, -0.8393), (-0.218099, 0.959568, -0.177939), (0.852288, 0.098452, -0.513725)154.561, 165.893, 188.853
91generate(-0.768594, 0.021283, -0.639383), (0.020108, -0.998149, -0.057397), (-0.639421, -0.056972, 0.766743)154.561, 165.893, 188.853
92generate(-0.77645, 0.432411, 0.458418), (0.44803, -0.132782, 0.884103), (0.443165, 0.891846, -0.090635)154.561, 165.893, 188.853
93generate(-0.090216, 0.932452, -0.34985), (0.925967, -0.050798, -0.374171), (-0.366669, -0.357706, -0.858837)154.561, 165.893, 188.853
94generate(0.304133, 0.809152, 0.502768), (0.814702, -0.494454, 0.302945), (0.493724, 0.317471, -0.809598)154.561, 165.893, 188.853
95generate(0.10991, 0.006879, -0.993918), (0.749992, -0.656786, 0.078391), (-0.652252, -0.754046, -0.077346)154.561, 165.893, 188.853
96generate(-0.773524, -0.511313, 0.37446), (0.626497, -0.706146, 0.329938), (0.095722, 0.489813, 0.866557)154.561, 165.893, 188.853
97generate(0.172539, -0.388318, -0.905229), (-0.383363, -0.873024, 0.301433), (-0.907338, 0.295022, -0.299498)154.561, 165.893, 188.853
98generate(-0.488206, -0.567142, 0.663329), (0.547604, 0.392753, 0.738834), (-0.679548, 0.723944, 0.118825)154.561, 165.893, 188.853
99generate(0.657559, 0.665652, 0.35288), (0.583354, -0.153436, -0.797594), (-0.476775, 0.730319, -0.489204)154.561, 165.893, 188.853
100generate(0.107887, -0.113071, 0.987712), (0.974602, -0.184085, -0.127529), (0.196243, 0.976385, 0.090339)154.561, 165.893, 188.853
101generate(0.89064, 0.301914, -0.340012), (0.300873, -0.951949, -0.057165), (-0.340933, -0.051387, -0.938682)154.561, 165.893, 188.853
102generate(-0.136061, -0.919921, -0.367739), (0.51615, -0.382656, 0.766266), (-0.845622, -0.08555, 0.526882)154.561, 165.893, 188.853
103generate(0.615509, -0.787611, -0.028575), (-0.787349, -0.616109, 0.022159), (-0.035059, 0.00886, -0.999346)154.561, 165.893, 188.853
104generate(0.560409, -0.640685, 0.524847), (0.065369, 0.665948, 0.743129), (-0.825632, -0.382148, 0.415084)154.561, 165.893, 188.853
105generate(0.919365, -0.347794, 0.183869), (0.297771, 0.309747, -0.902989), (0.257102, 0.884927, 0.388333)154.561, 165.893, 188.853
106generate(0.325502, -0.894876, 0.305361), (0.937114, 0.348336, 0.021892), (-0.125959, 0.279032, 0.951985)154.561, 165.893, 188.853
107generate(0.790021, -0.249329, 0.560092), (0.149556, -0.807596, -0.570458), (0.594559, 0.534438, -0.600729)154.561, 165.893, 188.853
108generate(0.830599, -0.505447, -0.23373), (-0.019259, -0.445542, 0.895054), (-0.556539, -0.738929, -0.379802)154.561, 165.893, 188.853
109generate(-0.051853, -0.624786, 0.779072), (-0.633556, -0.582451, -0.509272), (0.771958, -0.519993, -0.365635)154.561, 165.893, 188.853
110generate(0.920245, 0.313416, 0.23435), (-0.332242, 0.309257, 0.891053), (0.206796, -0.897848, 0.388722)154.561, 165.893, 188.853
111generate(0.333395, -0.707337, -0.623315), (0.463884, 0.698647, -0.544705), (0.820768, -0.107544, 0.561048)154.561, 165.893, 188.853
112generate(0.656242, -0.455835, -0.601299), (0.754045, 0.367021, 0.544712), (-0.027609, -0.81087, 0.584575)154.561, 165.893, 188.853
113generate(-0.052896, -0.88505, 0.46248), (0.505155, -0.423217, -0.752134), (0.861406, 0.193839, 0.469474)154.561, 165.893, 188.853
114generate(0.790564, 0.159322, 0.591291), (-0.239814, -0.807898, 0.538321), (0.563469, -0.567377, -0.600488)154.561, 165.893, 188.853
115generate(-0.907276, -0.124862, 0.401572), (-0.134519, -0.818565, -0.55844), (0.398441, -0.560679, 0.725868)154.561, 165.893, 188.853
116generate(0.094021, 0.976625, 0.193295), (-0.095745, -0.184385, 0.97818), (0.990956, -0.110476, 0.076171)154.561, 165.893, 188.853
117generate(-0.29056, 0.083898, -0.953171), (0.85213, 0.475818, -0.217878), (0.435257, -0.875533, -0.209746)154.561, 165.893, 188.853
118generate(0.643035, 0.597313, -0.479295), (0.67839, -0.153852, 0.718412), (0.355376, -0.787113, -0.504143)154.561, 165.893, 188.853
119generate(-0.473228, -0.726706, -0.497951), (0.876245, -0.330011, -0.351124), (0.090835, -0.602488, 0.792942)154.561, 165.893, 188.853
120generate(-0.200838, 0.155696, 0.967173), (0.159285, -0.968961, 0.18906), (0.966588, 0.192027, 0.169804)154.561, 165.893, 188.853

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Components

#1: Protein PHAGE COAT PROTEIN


Mass: 13906.811 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: THE BACTERIOPHAGE WAS GROWN IN THE HOST PSEUDOMONAS AERUGINOSA
Source: (natural) BACTERIOPHAGE PP7 (virus) / References: UniProt: Q38062
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 30

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Sample preparation

CrystalDescription: DATA WAS COLLECTED AT TWO OCCASIONS. PART OF THE DATA WAS COLLECTED AT STATION 9.6 AT SRS IN DARESBURY, USING THE QUANTUM4 CCD DETECTOR. THE REST OF THE DATA WAS COLLECTED AT MAXII IN ...Description: DATA WAS COLLECTED AT TWO OCCASIONS. PART OF THE DATA WAS COLLECTED AT STATION 9.6 AT SRS IN DARESBURY, USING THE QUANTUM4 CCD DETECTOR. THE REST OF THE DATA WAS COLLECTED AT MAXII IN LUND USING A MAR345 IMAGE PLATE DETECTOR
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temperature: 310 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlphage1drop
20.1 Msodium citrate1reservoir
33.0 M1,6-hexanediol1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorDate: Aug 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 606783 / % possible obs: 30 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.27
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 1 % / Rmerge(I) obs: 0.78 / % possible all: 1.7
Reflection
*PLUS
Rmerge(I) obs: 0.27
Reflection shell
*PLUS
Highest resolution: 3.4 Å / % possible obs: 1.7 % / Rmerge(I) obs: 0.782

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MS2

2ms2


Resolution: 3.5→60 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: RESIDUAL
RfactorNum. reflection% reflection
Rfree0.292 -5 %
Rwork0.288 --
obs0.288 602386 35.2 %
Refinement stepCycle: LAST / Resolution: 3.5→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 0 0 2904
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.31.5
X-RAY DIFFRACTIONc_mcangle_it4.12
X-RAY DIFFRACTIONc_scbond_it3.12
X-RAY DIFFRACTIONc_scangle_it5.32.5
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM

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