[日本語] English
万見
- PDB-1m06: Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crysta... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 1m06
タイトルStructural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography
要素
  • 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'
  • Capsid Protein
  • Major spike protein
  • Small core protein
キーワードVirus/DNA / Bacteriophage / three-dimensional structure / virion / morphogenesis / phiX174 / assembly / microviridae / Icosahedral virus / Virus-DNA COMPLEX
機能・相同性
機能・相同性情報


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
類似検索 - 分子機能
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
類似検索 - ドメイン・相同性
DNA / DNA-binding protein J / Capsid protein F / Major spike protein G / DNA-binding protein J
類似検索 - 構成要素
生物種Enterobacteria phage alpha3 (ファージ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.5 Å
データ登録者Bernal, R.A. / Hafenstein, S. / Olson, N.H. / Bowman, V. / Chipman, P.R. / Baker, T.S. / Fane, B.A. / Rossmann, M.G.
引用ジャーナル: J Mol Biol / 年: 2003
タイトル: Structural studies of bacteriophage alpha3 assembly.
著者: Ricardo A Bernal / Susan Hafenstein / Norman H Olson / Valorie D Bowman / Paul R Chipman / Timothy S Baker / Bentley A Fane / Michael G Rossmann /
要旨: 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.
履歴
登録2002年6月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02002年12月25日Provider: repository / タイプ: Initial release
改定 1.12008年4月1日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32011年12月28日Group: Advisory
改定 1.42017年10月11日Group: Refinement description / カテゴリ: software
改定 2.02023年4月19日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: 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
詳細: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / タイプ: Remediation
改定 2.12024年4月3日Group: Data collection / Refinement description
カテゴリ: 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.

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
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'


分子量 (理論値)分子数
合計 (水以外)73,4814
ポリマ－73,4814
非ポリマー00
水00
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


分子量 (理論値)分子数
合計 (水以外)4,408,837240
ポリマ－4,408,837240
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation59
2


  • 登録構造と同一
  • icosahedral asymmetric unit
タイプ名称対称操作数
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 ポリマー
分子量 (理論値)分子数
合計 (水以外)367,40320
ポリマ－367,40320
非ポリマー00
水0
タイプ名称対称操作数
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 ポリマー
分子量 (理論値)分子数
合計 (水以外)440,88424
ポリマ－440,88424
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation5
5


  • 登録構造と同一（異なる座標系）
  • icosahedral asymmetric unit, std point frame
タイプ名称対称操作数
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 ポリマー
分子量 (理論値)分子数
合計 (水以外)4,408,837240
ポリマ－4,408,837240
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z2
point symmetry operation59
単位格子
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
対称性点対称性: (ヘルマン・モーガン記号: 532 / シェーンフリース記号: I (正20面体型対称))
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
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

-
要素

#1: タンパク質 Capsid Protein / F protein / GPF


分子量: 49294.277 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Enterobacteria phage alpha3 (ファージ)
属: Microvirus / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P08767
#2: タンパク質 Major spike protein / G protein / GPG


分子量: 19598.990 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Enterobacteria phage alpha3 (ファージ)
属: Microvirus / 参照: UniProt: P31281
#3: タンパク質・ペプチド Small core protein / J protein


分子量: 2831.353 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Enterobacteria phage alpha3 (ファージ)
属: Microvirus / 参照: UniProt: P08766, UniProt: P69548*PLUS
#4: DNA鎖 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR))-3'


分子量: 1756.000 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: ssDNA FRAGMENT
由来: (組換発現) Enterobacteria phage alpha3 (ファージ)
属: Microvirus

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶化温度: 318.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5
詳細: 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
結晶化
*PLUS
温度: 45 ℃ / pH: 7.5
溶液の組成
*PLUS
ID濃度一般名Crystal-IDSol-ID詳細化学式
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

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 14-BM-C / 波長: 1 Å
検出器タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1998年9月9日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.5→100 Å / Num. obs: 597062 / % possible obs: 75.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / 冗長度: 4 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20
反射 シェル解像度: 3.5→3.63 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 18 / Num. unique all: 43298 / % possible all: 54.6
反射
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.08
反射 シェル
*PLUS
% possible obs: 55 %

-
解析

ソフトウェア
名称バージョン分類
JBluIce-EPICSデータ収集
SnB位相決定
ENVELOPEモデル構築
CNS1.1精密化
ENVELOPE位相決定
精密化構造決定の手法: 分子置換
開始モデル: Phix174 virion

解像度: 3.5→82.45 Å / Rfactor Rfree error: 0.001 / Isotropic thermal model: GROUP / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
詳細: 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 ...詳細: 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.
Rfactor反射数%反射Selection details
Rfree0.234 59662 10 %RANDOM
Rwork0.232 ---
all-597050 --
obs-597050 74.6 %-
溶媒の処理溶媒モデル: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.308565 e/Å3
原子変位パラメータ
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
精密化ステップサイクル: LAST / 解像度: 3.5→82.45 Å
タンパク質核酸リガンド溶媒全体
原子数4983 110 0 0 5093
拘束条件
Refine-IDタイプDev 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精密化 シェル解像度: 3.5→3.66 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 8
Rfactor反射数%反射
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
精密化
*PLUS
最高解像度: 3.5 Å / Num. reflection obs: 59662 / Rfactor Rwork: 0.23
溶媒の処理
*PLUS
原子変位パラメータ
*PLUS
拘束条件
*PLUS
Refine-IDタイプDev 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

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る