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- PDB-2w4y: Caulobacter bacteriophage 5 - virus-like particle -

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Basic information

Entry
Database: PDB / ID: 2w4y
TitleCaulobacter bacteriophage 5 - virus-like particle
ComponentsCAULOBACTER 5 VIRUS-LIKE PARTICLE
KeywordsVIRUS / ASSEMBLY / CALCIUM ION / RNA
Function / homologyPorin - #220 / Porin / Beta Barrel / Mainly Beta / ADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesUNCLASSIFIED LEVIVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPlevka, P. / Kazaks, A. / Dishlers, A. / Liljas, L. / Tars, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The Structure of Bacteriophage Phicb5 Reveals a Role of the RNA Genome and Metal Ions in Particle Stability and Assembly.
Authors: Plevka, P. / Kazaks, A. / Voronkova, T. / Kotelovica, S. / Dishlers, A. / Liljas, L. / Tars, K.
History
DepositionDec 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_conn_angle / 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_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAULOBACTER 5 VIRUS-LIKE PARTICLE
B: CAULOBACTER 5 VIRUS-LIKE PARTICLE
C: CAULOBACTER 5 VIRUS-LIKE PARTICLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,69910
Polymers40,4973
Non-polymers1,2027
Water0
1
A: CAULOBACTER 5 VIRUS-LIKE PARTICLE
B: CAULOBACTER 5 VIRUS-LIKE PARTICLE
C: CAULOBACTER 5 VIRUS-LIKE PARTICLE
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)2,501,935600
Polymers2,429,817180
Non-polymers72,119420
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: CAULOBACTER 5 VIRUS-LIKE PARTICLE
B: CAULOBACTER 5 VIRUS-LIKE PARTICLE
C: CAULOBACTER 5 VIRUS-LIKE PARTICLE
hetero molecules
x 5


  • icosahedral pentamer
  • 208 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)208,49550
Polymers202,48515
Non-polymers6,01035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CAULOBACTER 5 VIRUS-LIKE PARTICLE
B: CAULOBACTER 5 VIRUS-LIKE PARTICLE
C: CAULOBACTER 5 VIRUS-LIKE PARTICLE
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 250 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)250,19460
Polymers242,98218
Non-polymers7,21242
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
Unit cell
Length a, b, c (Å)406.400, 342.600, 409.700
Angle α, β, γ (deg.)90.00, 93.19, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.982559, -0.176189, 0.059465), (0.112802, 0.310508, -0.943854), (0.147833, 0.9341, 0.324967)-4.43038, 85.97807, 55.08026
3generate(0.954338, -0.172278, 0.244049), (0.006328, -0.805113, -0.593088), (0.298663, 0.567551, -0.767259)-20.65656, 60.18751, 152.63665
4generate(0.954338, 0.006328, 0.298663), (-0.172278, -0.805113, 0.567551), (0.244049, -0.593088, -0.767259)-26.25451, -41.73001, 157.84956
5generate(0.982559, 0.112802, 0.147833), (-0.176189, 0.310508, 0.9341), (0.059465, -0.943854, 0.324967)-13.48805, -78.92794, 63.51492
6generate(0.683442, 0.527332, -0.504805), (0.527332, -0.834815, -0.158128), (-0.504805, -0.158128, -0.848627)81.95802, -34.12572, 237.66789
7generate(0.656379, -0.428212, -0.621129), (0.400589, -0.499835, 0.767915), (-0.639292, -0.752861, -0.156544)96.46433, -116.94754, 179.56621
8generate(0.504804, -0.828807, 0.241355), (0.450743, 0.491526, 0.745139), (-0.736209, -0.267361, 0.621703)22.52753, -119.40022, 109.04653
9generate(0.438189, -0.120843, 0.890723), (0.608482, 0.769241, -0.19498), (-0.661619, 0.627427, 0.410604)-37.67425, -38.09423, 123.56465
10generate(0.548593, 0.717297, 0.429571), (0.655817, -0.050483, -0.75323), (-0.518604, 0.694936, -0.49811)-0.94418, 14.60831, 203.05702
11generate(-0.690343, -0.435485, 0.577736), (-0.435485, -0.387557, -0.812498), (0.577736, -0.812498, 0.0779)102.12524, 124.84806, 39.37033
12generate(-0.642018, 0.526073, 0.557728), (-0.591721, -0.802565, 0.075866), (0.487525, -0.281312, 0.826549)99.56342, 48.70345, -28.7555
13generate(-0.489027, 0.79744, -0.35347), (-0.660716, -0.074082, 0.746972), (0.56948, 0.598833, 0.563109)178.35834, -13.49931, -9.57555
14generate(-0.442799, 0.003597, -0.896613), (-0.547122, 0.791154, 0.273374), (0.710343, 0.611607, -0.348354)229.61809, 24.20188, 70.40413
15generate(-0.567219, -0.758393, -0.321096), (-0.407922, 0.597416, -0.690431), (0.715446, -0.260643, -0.64823)182.50345, 109.70525, 100.65435
16generate(-0.993099, -0.091847, -0.072931), (-0.091847, 0.222372, 0.970626), (-0.072931, 0.970626, -0.229273)197.71674, -90.72237, 132.96181
17generate(-0.99692, 0.078329, 0.003935), (0.078329, 0.991892, 0.100073), (0.003935, 0.100073, -0.994972)190.20263, -17.73401, 204.10905
18generate(-0.970115, 0.203644, -0.131934), (0.203644, 0.387668, -0.899023), (-0.131934, -0.899023, -0.417554)201.5707, 72.71199, 157.89239
19generate(-0.949727, 0.110917, -0.292773), (0.110917, -0.755283, -0.645946), (-0.292773, -0.645946, 0.70501)216.11066, 55.62234, 58.18168
20generate(-0.963932, -0.071706, -0.256307), (-0.071706, -0.857441, 0.509561), (-0.256307, 0.509561, 0.821373)213.72878, -45.38565, 42.77373
21generate(0.283995, -0.216957, 0.933957), (0.862839, -0.366975, -0.347617), (0.418157, 0.904577, 0.08298)-27.38795, -46.72721, 54.08143
22generate(0.392638, 0.755005, 0.525169), (0.755005, -0.590681, 0.284715), (0.525169, 0.284715, -0.801957)4.14288, -101.2486, 134.57315
23generate(0.548593, 0.655817, -0.518604), (0.717297, -0.050483, 0.694936), (0.429571, -0.75323, -0.49811)96.2437, -139.69699, 112.55376
24generate(0.536336, -0.377447, -0.754903), (0.801826, 0.507084, 0.316134), (0.263476, -0.774854, 0.574614)121.6343, -108.93801, 18.45331
25generate(0.372805, -0.916851, 0.142829), (0.891776, 0.311481, -0.3282), (0.256422, 0.249726, 0.933748)45.22574, -51.47954, -17.68458
26generate(-0.391781, 0.183194, -0.901636), (0.571661, 0.816327, -0.082539), (0.72091, -0.547768, -0.424546)225.26321, -46.10485, 77.20518
27generate(-0.497574, -0.716307, -0.489207), (0.641572, 0.075656, -0.763322), (0.583785, -0.693672, 0.421918)193.08724, 17.00248, 3.53113
28generate(-0.642018, -0.59172, 0.487525), (0.526073, -0.802565, -0.281312), (0.557728, 0.075866, 0.826549)106.75931, -21.37915, -35.45646
29generate(-0.625495, 0.384779, 0.67875), (0.384779, -0.604665, 0.69737), (0.67875, 0.69737, 0.23016)85.58169, -108.20762, 14.12194
30generate(-0.47084, 0.863702, -0.179799), (0.412954, 0.395866, 0.820219), (0.779601, 0.311943, -0.543059)158.82112, -123.48894, 83.75066
31generate(0.438009, -0.79843, 0.413107), (-0.636674, 0.048908, 0.769581), (-0.634661, -0.600097, -0.486917)11.2986, -18.1115, 212.98743
32generate(0.401375, 0.060791, 0.913894), (-0.506283, 0.846226, 0.166066), (-0.763266, -0.529344, 0.370432)-36.53543, 31.30296, 137.38446
33generate(0.536336, 0.801826, 0.263476), (-0.377447, 0.507084, -0.774854), (-0.754903, 0.316134, 0.574614)17.25053, 115.44988, 115.65752
34generate(0.656379, 0.400589, -0.639292), (-0.428212, -0.499835, -0.752861), (-0.621129, 0.767915, -0.156544)98.3261, 118.04107, 177.83251
35generate(0.59561, -0.588423, -0.546815), (-0.588423, -0.783003, 0.201653), (-0.546815, 0.201653, -0.812606)94.64761, 35.4956, 237.9857
36generate(-0.330223, 0.832194, -0.445428), (-0.797827, -0.498261, -0.339424), (-0.504406, 0.243289, 0.828484)172.62614, 110.94353, 65.72599
37generate(-0.296439, -0.099489, -0.949856), (-0.890294, -0.331202, 0.312541), (-0.345688, 0.9383, 0.009606)221.10531, 52.94313, 134.51129
38generate(-0.442911, -0.865923, -0.232397), (-0.865923, 0.345964, 0.36123), (-0.232397, 0.36123, -0.903053)161.54646, 45.62623, 217.24519
39generate(-0.567219, -0.407922, 0.715446), (-0.758393, 0.597416, -0.260643), (-0.321096, -0.690431, -0.64823)76.25791, 99.10453, 199.59227
40generate(-0.497574, 0.641572, 0.583785), (-0.716307, 0.075656, -0.693672), (-0.489208, -0.763322, 0.421918)83.10553, 139.47285, 105.94825
41generate(0.283995, 0.862839, 0.418157), (-0.216957, -0.366975, 0.904577), (0.933957, -0.347617, 0.08298)25.48157, -72.01053, 4.8483
42generate(0.438189, 0.608482, -0.661619), (-0.120843, 0.769241, 0.627427), (0.890723, -0.19498, 0.410604)121.44082, -52.77683, -24.6064
43generate(0.401375, -0.506283, -0.763266), (0.060791, 0.846226, -0.529344), (0.913894, 0.166066, 0.370432)135.37347, 48.45528, -22.70045
44generate(0.22443, -0.94089, 0.253689), (0.076932, -0.24241, -0.967119), (0.971449, 0.236567, 0.017981)48.02508, 91.78647, 7.93218
45generate(0.151884, -0.094725, 0.983849), (-0.094725, -0.99221, -0.080907), (0.983849, -0.080907, -0.159674)-19.89186, 17.3345, 24.95825
46generate(0.438009, -0.636674, -0.634661), (-0.79843, 0.048908, -0.600097), (0.413107, 0.769581, -0.486917)118.69478, 137.72016, 112.97802
47generate(0.264728, -0.867702, 0.420729), (-0.867702, -0.404689, -0.288653), (0.420729, -0.288653, -0.860038)27.05696, 112.40904, 150.49532
48generate(0.22443, 0.076932, 0.971449), (-0.94089, -0.24241, 0.236567), (0.253689, -0.967119, 0.017981)-25.54531, 65.5598, 76.44235
49generate(0.372805, 0.891776, 0.256422), (-0.916851, 0.311481, 0.249726), (0.142829, -0.3282, 0.933748)33.58254, 61.91649, -6.8422
50generate(0.504804, 0.450743, -0.736209), (-0.828807, 0.491526, -0.267361), (0.241355, 0.745139, 0.621703)122.72782, 106.51405, 15.73808
51generate(-0.330223, -0.797827, -0.504406), (0.832194, -0.498261, 0.243289), (-0.445428, -0.339424, 0.828484)178.67139, -104.37001, 60.09652
52generate(-0.489027, -0.660716, 0.56948), (0.79744, -0.074082, 0.598833), (-0.35347, 0.746972, 0.563109)83.75599, -137.49605, 78.51999
53generate(-0.47084, 0.412954, 0.779601), (0.863702, 0.395866, 0.311943), (-0.179799, 0.820219, -0.543059)60.48261, -114.41459, 175.3254
54generate(-0.300796, 0.939408, -0.164422), (0.939408, 0.262131, -0.220908), (-0.164422, -0.220908, -0.961335)141.01427, -67.02342, 216.73097
55generate(-0.213889, 0.191104, -0.957983), (0.919935, -0.29047, -0.263339), (-0.32859, -0.937607, -0.113675)214.05895, -60.81553, 145.51561
56generate(-0.391781, 0.571661, 0.72091), (0.183194, 0.816327, -0.547768), (-0.901636, -0.082539, -0.424546)58.95226, 38.66035, 232.07718
57generate(-0.213889, 0.919935, -0.32859), (0.191104, -0.29047, -0.937607), (-0.957983, -0.263339, -0.113675)149.54624, 77.86381, 205.59111
58generate(-0.154965, 0.016396, -0.987784), (0.016396, -0.999682, -0.019166), (-0.987784, -0.019166, 0.154646)211.48923, 0.39948, 180.93273
59generate(-0.296439, -0.890294, -0.345688), (-0.099489, -0.331202, 0.9383), (-0.949856, 0.312541, 0.009606)159.17812, -86.67956, 192.17908
60generate(-0.442799, -0.547122, 0.710343), (0.003597, 0.791154, 0.611607), (-0.896613, 0.273374, -0.348354)64.90509, -63.03304, 223.78809
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I).

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Components

#1: Protein CAULOBACTER 5 VIRUS-LIKE PARTICLE


Mass: 13498.981 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: LEVIVIRUS COAT PROTEIN / Source: (gene. exp.) UNCLASSIFIED LEVIVIRUS / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.87 Å3/Da / Density % sol: 79 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS-HCL PH 8.0, 5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9814
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 9, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 720797 / % possible obs: 59 % / Observed criterion σ(I): 0.5 / Redundancy: 1.5 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 3.9
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 0.7 / % possible all: 39

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 2.9→50 Å / Cross valid method: NONE / σ(F): 0
Stereochemistry target values: STANDARD CRYSTALLOGRAPHIC RESIDUAL
RfactorNum. reflection% reflection
Rwork0.278 --
obs0.278 720797 59 %
Solvent computationBsol: 15.81 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.014 Å20 Å21.824 Å2
2---4.183 Å20 Å2
3---0.169 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.49 Å
Luzzati d res low-50 Å
Luzzati sigma a0.69 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 70 0 2932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.45
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
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: 2.9→3.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.384 55713 -
obs--39 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_PARAMPROTEIN_TOP
X-RAY DIFFRACTION2ION_PARAMION_TOP
X-RAY DIFFRACTION3DNA-RNA_REP_PARAMDNA-RNA-ALLATOM_TOP

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