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- PDB-1m06: Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crysta... -

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Database: PDB / ID: 1m06
TitleStructural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography
Components
  • 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'
  • Capsid ProteinCapsid
  • Major spike protein
  • Small core protein
KeywordsVirus/DNA / Bacteriophage / three-dimensional structure / virion / morphogenesis / phiX174 / assembly / microviridae / Icosahedral virus / Virus-DNA COMPLEX
Function / homology
Function and homology information


modulation by virus of host process / T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Microvirus J protein-like / Microvirus J protein / Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus ...Microvirus J protein-like / Microvirus J protein / Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA-binding protein J / Capsid protein F / Major spike protein G / DNA-binding protein J
Similarity search - Component
Biological speciesEnterobacteria phage alpha3 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBernal, R.A. / Hafenstein, S. / Olson, N.H. / Bowman, V. / Chipman, P.R. / Baker, T.S. / Fane, B.A. / Rossmann, M.G.
CitationJournal: J Mol Biol / Year: 2003
Title: Structural studies of bacteriophage alpha3 assembly.
Authors: Ricardo A Bernal / Susan Hafenstein / Norman H Olson / Valorie D Bowman / Paul R Chipman / Timothy S Baker / Bentley A Fane / Michael G Rossmann /
Abstract: Bacteriophage alpha3 is a member of the Microviridae, a family of small, single-stranded, icosahedral phages that include phiX174. These viruses have an ssDNA genome associated with approximately 12 ...Bacteriophage alpha3 is a member of the Microviridae, a family of small, single-stranded, icosahedral phages that include phiX174. These viruses have an ssDNA genome associated with approximately 12 copies of an H pilot protein and 60 copies of a small J DNA-binding protein. The surrounding capsid consists of 60 F coat proteins decorated with 12 pentameric spikes of G protein. Assembly proceeds via a 108S empty procapsid that requires the external D and internal B scaffolding proteins for its formation. The alpha3 "open" procapsid structural intermediate was determined to 15A resolution by cryo-electron microscopy (cryo-EM). Unlike the phiX174 "closed" procapsid and the infectious virion, the alpha3 open procapsid has 30A wide pores at the 3-fold vertices and 20A wide gaps between F pentamers as a result of the disordering of two helices in the F capsid protein. The large pores are probably used for DNA entry and internal scaffolding protein exit during DNA packaging. Portions of the B scaffolding protein are located at the 5-fold axes under the spike and in the hydrophobic pocket on the inner surface of the capsid. Protein B appears to have autoproteolytic activity that cleaves at an Arg-Phe motif and probably facilitates the removal of the protein through the 30A wide pores. The structure of the alpha3 mature virion was solved to 3.5A resolution by X-ray crystallography and was used to interpret the open procapsid cryo-EM structure. The main differences between the alpha3 and phiX174 virion structures are in the spike and the DNA-binding proteins. The alpha3 pentameric spikes have a rotation of 3.5 degrees compared to those of phiX174. The alpha3 DNA-binding protein, which is shorter by 13 amino acid residues at its amino end when compared to the phiX174 J protein, retains its carboxy-terminal-binding site on the internal surface of the capsid protein. The icosahedrally ordered structural component of the ssDNA appears to be substantially increased in alpha3 compared to phiX174, allowing the building of about 10% of the ribose-phosphate backbone.
History
DepositionJun 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Residue 160 of the F protein is an ARG according to the reported sequence but no density ...SEQUENCE Residue 160 of the F protein is an ARG according to the reported sequence but no density is seen for the side chain in the crystal structure for this residue. After a structural sequence alignment with homologous bacteriophages phix174 and G4, residue 160 was found to be a glycine in the other phages. Consequently, the authors state residue 160 should be a Glycine.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Capsid Protein
G: Major spike protein
J: Small core protein
X: 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'


Theoretical massNumber of molelcules
Total (without water)73,4814
Polymers73,4814
Non-polymers00
Water0
1
F: Capsid Protein
G: Major spike protein
J: Small core protein
X: 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'
x 60


Theoretical massNumber of molelcules
Total (without water)4,408,837240
Polymers4,408,837240
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
F: Capsid Protein
G: Major spike protein
J: Small core protein
X: 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'
x 5


  • icosahedral pentamer
  • 367 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)367,40320
Polymers367,40320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
F: Capsid Protein
G: Major spike protein
J: Small core protein
X: 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'
x 6


  • icosahedral 23 hexamer
  • 441 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)440,88424
Polymers440,88424
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
F: Capsid Protein
G: Major spike protein
J: Small core protein
X: 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'
x 60


  • crystal asymmetric unit, crystal frame
  • 4.41 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,408,837240
Polymers4,408,837240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)290.258, 332.115, 337.698
Angle α, β, γ (deg.)90.00, 94.08, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.48018149, 0.41487391, -0.77285593), (0.17537847, 0.81788107, 0.54800848), (0.85945744, -0.3986852, 0.31997142)65.21148, -42.73516, 33.49493
3generate(-0.36090257, 0.84665852, -0.3910485), (0.6986422, 0.52320654, 0.48801052), (0.61777658, -0.09707848, -0.78033795)52.90836, -47.89524, 117.29672
4generate(-0.3609026, 0.69864217, 0.61777741), (0.84665849, 0.52320658, -0.09707872), (-0.39104786, 0.48800993, -0.78033797)-19.90686, -8.34919, 135.59414
5generate(0.48018145, 0.17537842, 0.85945867), (0.41487387, 0.81788114, -0.39868582), (-0.77285478, 0.54800773, 0.31997139)-52.60602, 21.2517, 63.10078
6generate(-0.99943578, -0.03358711, -0.00026696), (-0.03358621, 0.99930946, 0.01589126), (-0.00026695, 0.01589117, -0.99987369)135.35701, 0.94323, 167.40818
7generate(-0.48603046, -0.44200366, 0.75392843), (0.17278775, 0.79704664, 0.57867211), (-0.8566901, 0.41152118, -0.31101619)71.60874, -43.42035, 133.22096
8generate(0.33706865, -0.8637279, 0.37464532), (0.72009836, 0.4928665, 0.48840682), (-0.60649996, 0.10515456, 0.78809883)84.05585, -46.83194, 49.35104
9generate(0.33236655, -0.71595126, -0.61395993), (0.85198095, 0.50713564, -0.13016105), (0.40454921, -0.47982043, 0.77853179)155.49687, -4.57684, 31.7038
10generate(-0.49363861, -0.20289603, -0.84566846), (0.38617827, 0.8201346, -0.42219173), (0.77922181, -0.53498824, -0.326496)187.20273, 24.94984, 104.66712
11generate(0.89684746, 0.02835718, 0.4414304), (0.02835631, -0.99957608, 0.00659902), (0.44142979, 0.00659921, -0.89727138)-32.75551, 163.58584, 130.24333
12generate(0.81501343, 0.21927965, -0.53634879), (-0.15601637, -0.808401, -0.56758001), (-0.55804279, 0.5462639, -0.62464641)39.30307, 208.37308, 128.69356
13generate(-0.03115767, 0.73130682, -0.68133715), (-0.70450318, -0.49961726, -0.50404181), (-0.7090159, 0.46429878, 0.53077493)65.11539, 213.73511, 48.0356
14generate(-0.47228615, 0.85683454, 0.20683432), (-0.85911398, -0.49995348, 0.10940599), (0.19715018, -0.12602312, 0.97223963)9.00969, 172.2618, -0.26398
15generate(0.10125257, 0.42238777, 0.90074282), (-0.40618191, -0.80894502, 0.42499939), (0.90816471, -0.40889702, 0.08965848)-51.47784, 141.26784, 50.54319
16generate(-0.89741169, 0.00522993, -0.44116344), (0.0052299, -0.99973338, -0.02249028), (-0.44116284, -0.02249038, 0.89714507)162.56489, 167.58597, 39.78961
17generate(-0.80916446, -0.1921499, 0.5552763), (-0.19214985, -0.80652672, -0.55910058), (0.55527545, -0.55909988, 0.61569118)89.04311, 209.89748, 42.03167
18generate(0.0549916, -0.71423744, 0.69774033), (-0.71423738, -0.51645578, -0.47237553), (0.69773928, -0.47237487, -0.53853582)63.0868, 213.10711, 122.75776
19generate(0.5008222, -0.83952545, -0.2106518), (-0.83952547, -0.53038874, 0.11783378), (-0.21065152, 0.11783362, -0.97043345)120.5667, 172.77928, 170.40717
20generate(-0.08779541, -0.39487016, -0.91453303), (-0.39487023, -0.82907071, 0.39587816), (-0.91453174, 0.39587753, -0.08313387)182.04754, 144.64566, 119.13003
21generate(0.20040269, 0.23744288, -0.95050553), (0.97680544, 0.02626854, 0.21251041), (0.0754269, -0.97104595, -0.22667122)113.47691, -1.83372, 179.1069
22generate(-0.67904703, 0.65629438, -0.3288963), (0.65629448, 0.34201088, -0.67253724), (-0.32889622, -0.67253699, -0.66296385)84.56119, 67.86064, 217.93107
23generate(-0.49363828, 0.38617794, 0.77922299), (-0.20289533, 0.82013434, -0.53498892), (-0.84566761, -0.42219187, -0.32649606)1.21633, 73.51609, 203.01831
24generate(0.50040035, -0.19961469, 0.84246915), (-0.41339288, 0.79988854, 0.43506828), (-0.76072677, -0.56597902, 0.3177451)-21.37791, 7.317, 154.97755
25generate(0.92934125, -0.29153802, -0.22656187), (0.31570229, 0.30925249, 0.89704827), (-0.19145905, -0.90518949, 0.37944025)48.00294, -39.25174, 140.19948
26generate(-0.20801068, 0.21544333, 0.95410524), (-0.97719329, -0.00318063, -0.2123269), (-0.04271008, -0.97651084, 0.21119131)-18.29562, 165.98451, 150.45393
27generate(0.7579141, -0.29047882, 0.58411347), (-0.65227388, -0.32336179, 0.68554808), (-0.01025762, -0.90058789, -0.43455231)-9.10962, 95.28434, 196.47392
28generate(0.81501326, -0.15601574, -0.55804365), (0.21927886, -0.80840079, 0.54626453), (-0.53634847, -0.56757984, -0.62464645)72.29358, 89.5299, 219.73648
29generate(-0.1156223, 0.43300917, -0.89394381), (0.43300867, -0.78799021, -0.43769243), (-0.89394294, -0.43769251, -0.09638749)113.41752, 156.67363, 188.09353
30generate(-0.74788586, 0.6625835, 0.0406156), (-0.30645179, -0.29033678, -0.90652771), (-0.58885763, -0.69042576, 0.42018866)57.43032, 203.92517, 145.27456
31generate(-0.23311782, -0.23793196, 0.94289214), (0.97059879, 0.00284444, 0.24068545), (-0.05994829, 0.97127735, 0.23027337)21.9579, -1.85425, -11.73553
32generate(0.65670866, -0.6672317, 0.35147629), (0.67342133, 0.3090448, -0.67156178), (0.33946524, 0.67771179, 0.65228051)48.50611, 69.38012, -49.43955
33generate(0.50040019, -0.41339328, -0.76072744), (-0.19961452, 0.79988859, -0.56597907), (0.84246833, 0.43506834, 0.3177452)131.61798, 77.59392, -34.41655
34generate(-0.48603025, 0.17278721, -0.85669132), (-0.44200288, 0.79704637, 0.41152187), (0.7539278, 0.57867199, -0.31101612)156.43573, 11.43597, 12.57219
35generate(-0.9393693, 0.28122828, 0.19620348), (0.28122871, 0.30444599, 0.91006796), (0.19620366, 0.91006737, -0.36507669)88.66208, -37.6657, 26.58983
36generate(0.24072581, -0.21495425, -0.94649185), (-0.97021093, -0.02593235, -0.24086896), (0.02723147, 0.97627945, -0.21479346)148.0272, 169.8185, 19.61583
37generate(-0.73557573, 0.30141614, -0.60669347), (-0.67744193, -0.32769389, 0.65855094), (-0.0003114, 0.89541308, 0.44523565)141.20871, 99.58995, -27.52432
38generate(-0.82177517, 0.18323108, 0.5395481), (0.18323098, -0.81162214, 0.55470346), (0.53954775, 0.55470337, 0.63339731)60.03851, 91.47513, -50.89711
39generate(0.1012522, -0.40618169, 0.90816597), (0.42238709, -0.8089447, -0.40889772), (0.9007419, 0.42499954, 0.08965851)16.69106, 156.68845, -18.20214
40generate(0.75791392, -0.65227376, -0.01025721), (-0.29047921, -0.3233617, -0.90058852), (0.58411303, 0.68554788, -0.43455222)71.07106, 205.10731, 25.37725
41generate(0.20040305, 0.97680601, 0.07542748), (0.23744269, 0.02626816, -0.97104663), (-0.95050432, 0.21250979, -0.22667122)-34.45951, 147.02506, 148.84835
42generate(0.33236729, 0.85198133, 0.40454993), (-0.71595081, 0.50713493, -0.47982098), (-0.6139592, -0.13016125, 0.77853176)-60.60846, 128.86133, 70.19059
43generate(0.65670925, 0.67342186, 0.33946538), (-0.6672315, 0.30904428, 0.67771207), (0.3514756, -0.67156117, 0.65228046)-61.79348, 44.42906, 61.79273
44generate(0.72519937, 0.68789071, -0.02988153), (0.31627219, -0.29424925, 0.9018812), (0.611602, -0.66349369, -0.43095012)-36.37693, 10.41077, 135.26034
45generate(0.44318663, 0.87539243, -0.19306593), (0.87539158, -0.46901451, -0.11710771), (-0.19306584, -0.11710778, -0.97417213)-19.4836, 73.81858, 189.06367
46generate(-0.23311733, 0.97059916, -0.05994877), (-0.23793174, 0.00284395, 0.97127803), (0.94289113, 0.24068567, 0.23027338)6.21497, 16.62822, -17.55524
47generate(0.00676015, 0.72102108, 0.69288079), (0.72102048, -0.48361984, 0.49622667), (0.69288012, 0.49622659, -0.52314032)-52.47365, 33.52369, 41.35933
48generate(0.72519923, 0.31627279, 0.61160309), (0.68788989, -0.29424915, -0.66349438), (-0.02988117, 0.90188054, -0.43095009)-59.63776, 117.83115, 47.8142
49generate(0.92934152, 0.31570268, -0.19145885), (-0.29153817, 0.30925214, -0.90519006), (-0.22656121, 0.89704753, 0.37944032)-5.37682, 153.04056, -7.11105
50generate(0.33706931, 0.72009861, -0.60650073), (-0.8637274, 0.49286578, 0.10515485), (0.37464513, 0.48840662, 0.78809889)35.32241, 90.4937, -47.51159
51generate(0.24072552, -0.9702113, 0.02723105), (-0.21495418, -0.02593196, 0.97628011), (-0.94649082, -0.24086918, -0.21479355)128.59174, 17.07225, 185.22378
52generate(-0.03115831, -0.70450334, -0.70901701), (0.73130629, -0.49961658, 0.46429941), (-0.68133655, -0.50404168, 0.53077489)186.66405, 36.86341, 126.60081
53generate(-0.74788631, -0.30645213, -0.5888581), (0.66258334, -0.29033635, -0.69042598), (0.04061518, -0.90652702, 0.42018868)190.99076, 121.45585, 121.48841
54generate(-0.91896475, -0.32615092, 0.22165224), (-0.32615025, 0.31269056, -0.89210483), (0.22165162, -0.89210413, -0.39372581)135.5925, 153.94569, 176.95176
55generate(-0.30796903, -0.73637664, 0.60241628), (-0.86849826, 0.47610146, 0.13797618), (-0.38841344, -0.48070495, -0.78616641)97.02779, 89.43308, 216.34238
56generate(-0.20801124, -0.97719388, -0.04270975), (0.21544323, -0.00318014, -0.97651151), (0.95410401, -0.21232628, 0.21119138)164.8192, 151.38951, 20.92422
57generate(-0.30796913, -0.86849907, -0.38841371), (-0.73637596, 0.47610149, -0.48070509), (0.60241563, 0.13797633, -0.78616634)191.58446, 132.8666, 99.29039
58generate(-0.63402217, -0.68324252, -0.36221037), (-0.68324173, 0.27554123, 0.67620829), (-0.3622096, 0.67620765, -0.64151905)195.60689, 48.39898, 106.34578
59generate(-0.73557614, -0.67744248, -0.00031187), (0.30141623, -0.32769345, 0.89541369), (-0.6066924, 0.65855028, 0.44523561)171.32764, 14.71803, 32.34008
60generate(-0.47228691, -0.8591144, 0.19715038), (0.85683407, -0.49995274, -0.12602332), (0.20683415, 0.10940611, 0.97223964)152.2998, 78.36968, -20.45335

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Components

#1: Protein Capsid Protein / Capsid / F protein / GPF


Mass: 49294.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage alpha3 (virus) / Genus: Microvirus / Production host: Escherichia coli (E. coli) / References: UniProt: P08767
#2: Protein Major spike protein / G protein / GPG


Mass: 19598.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage alpha3 (virus) / Genus: Microvirus / References: UniProt: P31281
#3: Protein/peptide Small core protein / J protein


Mass: 2831.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage alpha3 (virus) / Genus: Microvirus / References: UniProt: P08766, UniProt: P69548*PLUS
#4: DNA chain 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'


Mass: 1756.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ssDNA FRAGMENT / Source: (gene. exp.) Enterobacteria phage alpha3 (virus) / Genus: Microvirus

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Experimental details

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Experiment

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

-
Sample preparation

Crystal growTemperature: 318.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 3-5% PEG8000, 100 mM sodium citrate pH 5.0, 1 mM EDTA, 300 mM NaCl, 0.1 mM-mercapto-ethanol, and 0.02 % sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 318.15K
Crystal grow
*PLUS
Temperature: 45 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris1droppH7.5
21 mMEDTA1drop
3300 mM1dropNaCl
40.1 mMbeta-mercaptoethanol1drop
50.02 %(w/v)sodium azide1drop
63-5 %PEG80001reservoir
7100 mMsodium citrate1reservoirpH5.0
840 %(v/v)glycerol1reservoir
90.02 %sodium azide1reservoir
100.1 %beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. obs: 597062 / % possible obs: 75.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 18 / Num. unique all: 43298 / % possible all: 54.6
Reflection
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 55 %

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
SnBphasing
ENVELOPEmodel building
CNS1.1refinement
ENVELOPEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phix174 virion

Resolution: 3.5→82.45 Å / Rfactor Rfree error: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: This bacteriophage has a single stranded DNA genome of 6087 nucleotides. In the asymmetric unit the authors can see non protein density which they have attributed to the ssDNA. This density ...Details: This bacteriophage has a single stranded DNA genome of 6087 nucleotides. In the asymmetric unit the authors can see non protein density which they have attributed to the ssDNA. This density is weak and there is no density for the base portion of the nucleotides because the sequence will be different in all the 60 subunits in the virus. The sugar-phosphate portion of a nucleotide was built in with no particular sequence in mind and is thus not necessarily a 10mer of CYTs. There is no particular connectivity associated with the DNA. It is all just fragments. The numbering of the nucleotides is irrellevant since they are all identical, have no bases, and the authors can see only about 10% of the entire genome. Only nucleotides 1, 2, 3, and 4 are linked, the others are not linked.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 59662 10 %RANDOM
Rwork0.232 ---
all-597050 --
obs-597050 74.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.308565 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å226.04 Å2
2---5.06 Å20 Å2
3---4.36 Å2
Refine analyzeLuzzati coordinate error free: 0.45 Å / Luzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 3.5→82.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 110 0 0 5093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
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_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
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: CONSTR
LS refinement shellResolution: 3.5→3.66 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.281 5469 10 %
Rwork0.275 49477 -
obs--55.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
Refinement
*PLUS
Highest resolution: 3.5 Å / Num. reflection obs: 59662 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25

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