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- PDB-6xb3: Structure of AcNPV poxin in post-reactive state with Gp[2'-5']Ap[3'] -

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基本情報

登録情報
データベース: PDB / ID: 6xb3
タイトルStructure of AcNPV poxin in post-reactive state with Gp[2'-5']Ap[3']
要素Poxin
キーワードHYDROLASE / Poxin / p26 / baculovirus / nucleopolyhedrovirus / innate immunity / nuclease / cGAS / cGAMP / STING
機能・相同性Nucleopolyhedrovirus p26 protein / Poxin, virus / nuclease activity / 2',3'-cyclic GMP-AMP binding / 加水分解酵素; エステル加水分解酵素 / 2',5'-GpAp / Poxin
機能・相同性情報
生物種Autographa californica nuclear polyhedrosis virus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.9 Å
データ登録者Eaglesham, J.B. / McCarty, K.L. / Kranzusch, P.J.
引用ジャーナル: Elife / 年: 2020
タイトル: Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host-pathogen conflict.
著者: Eaglesham, J.B. / McCarty, K.L. / Kranzusch, P.J.
履歴
登録2020年6月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年11月25日Provider: repository / タイプ: Initial release
改定 1.12024年3月6日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22024年4月3日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Poxin
B: Poxin
C: Poxin
D: Poxin
E: Poxin
F: Poxin
G: Poxin
H: Poxin
I: Poxin
J: Poxin
K: Poxin
L: Poxin
M: Poxin
N: Poxin
O: Poxin
P: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)449,47132
ポリマ－438,39216
非ポリマー11,07916
水60,0623334
1
A: Poxin
B: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,1844
ポリマ－54,7992
非ポリマー1,3852
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Poxin
D: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,1844
ポリマ－54,7992
非ポリマー1,3852
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Poxin
F: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,1844
ポリマ－54,7992
非ポリマー1,3852
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Poxin
H: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,1844
ポリマ－54,7992
非ポリマー1,3852
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I: Poxin
J: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,1844
ポリマ－54,7992
非ポリマー1,3852
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K: Poxin
L: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,1844
ポリマ－54,7992
非ポリマー1,3852
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
7
M: Poxin
N: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,1844
ポリマ－54,7992
非ポリマー1,3852
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
8
O: Poxin
P: Poxin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,1844
ポリマ－54,7992
非ポリマー1,3852
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)127.234, 127.192, 127.151
Angle α, β, γ (deg.)124.813, 102.390, 102.385
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 or resid 3 through 18...
d_2ens_1(chain "B" and (resid 1 or resid 3 through 18...
d_3ens_1(chain "C" and (resid 1 or resid 3 through 18...
d_4ens_1(chain "D" and (resid 1 or resid 3 through 18...
d_5ens_1(chain "E" and (resid 1 or resid 3 through 18...
d_6ens_1(chain "F" and (resid 1 or resid 3 through 18...
d_7ens_1(chain "G" and (resid 1 or resid 3 through 18...
d_8ens_1(chain "H" and (resid 1 or resid 3 through 18...
d_9ens_1(chain "I" and (resid 1 or resid 3 through 18...
d_10ens_1(chain "J" and (resid 1 or resid 3 through 18...
d_11ens_1(chain "K" and (resid 1 or resid 3 through 18...
d_12ens_1(chain "L" and (resid 1 or resid 3 through 18...
d_13ens_1(chain "M" and (resid 1 or resid 3 through 18...
d_14ens_1(chain "N" and (resid 1 or resid 3 through 18...
d_15ens_1(chain "O" and (resid 1 or resid 3 through 18...
d_16ens_1(chain "P" and (resid 1 or resid 3 through 18...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METMETA2
d_12ens_1LEUILEA4 - 19
d_13ens_1GLNGLNA21 - 36
d_14ens_1VALSERA38 - 71
d_15ens_1LEUASNA76 - 92
d_16ens_1ARGASNA94 - 107
d_17ens_1THRGLYA109 - 122
d_18ens_1LYSHISA124 - 133
d_19ens_1TRPVALA140 - 163
d_110ens_1VALGLUA165 - 166
d_111ens_1TRPARGA168 - 169
d_112ens_1ASNASPA171 - 183
d_113ens_1LYSGLUA186 - 191
d_114ens_1SERLYSA202 - 208
d_115ens_1SERASNA210 - 217
d_116ens_1GLYILEA219 - 233
d_21ens_1METMETB1
d_22ens_1LEUILEB3 - 18
d_23ens_1GLNGLNB20 - 35
d_24ens_1VALSERB37 - 70
d_25ens_1LEUASNB75 - 91
d_26ens_1ARGASNB93 - 106
d_27ens_1THRGLYB108 - 121
d_28ens_1LYSHISB123 - 132
d_29ens_1TRPVALB139 - 162
d_210ens_1VALGLUB164 - 165
d_211ens_1TRPARGB167 - 168
d_212ens_1ASNASPB170 - 182
d_213ens_1LYSGLUB185 - 190
d_214ens_1SERLYSB198 - 204
d_215ens_1SERASNB206 - 213
d_216ens_1GLYILEB215 - 229
d_31ens_1METMETC1
d_32ens_1LEUILEC3 - 18
d_33ens_1GLNGLNC20 - 35
d_34ens_1VALSERC37 - 70
d_35ens_1LEUASNC75 - 91
d_36ens_1ARGASNC93 - 106
d_37ens_1THRGLYC108 - 121
d_38ens_1LYSHISC123 - 132
d_39ens_1TRPVALC139 - 162
d_310ens_1VALGLUC164 - 165
d_311ens_1TRPARGC167 - 168
d_312ens_1ASNASPC170 - 182
d_313ens_1LYSGLUC185 - 190
d_314ens_1SERLYSC194 - 200
d_315ens_1SERASNC202 - 209
d_316ens_1GLYILEC211 - 225
d_41ens_1METMETD1
d_42ens_1LEUILED3 - 18
d_43ens_1GLNGLND20 - 35
d_44ens_1VALSERD37 - 70
d_45ens_1LEUASND75 - 91
d_46ens_1ARGASND93 - 106
d_47ens_1THRGLYD108 - 121
d_48ens_1LYSHISD123 - 132
d_49ens_1TRPVALD139 - 162
d_410ens_1VALGLUD164 - 165
d_411ens_1TRPARGD167 - 168
d_412ens_1ASNASPD170 - 182
d_413ens_1LYSGLUD185 - 190
d_414ens_1SERLYSD193 - 199
d_415ens_1SERASND201 - 208
d_416ens_1GLYILED210 - 224
d_51ens_1METMETE2
d_52ens_1LEUILEE4 - 19
d_53ens_1GLNGLNE21 - 36
d_54ens_1VALSERE38 - 71
d_55ens_1LEUASNE76 - 92
d_56ens_1ARGASNE94 - 107
d_57ens_1THRGLYE109 - 122
d_58ens_1LYSHISE124 - 133
d_59ens_1TRPVALE140 - 163
d_510ens_1VALGLUE165 - 166
d_511ens_1TRPARGE168 - 169
d_512ens_1ASNASPE171 - 183
d_513ens_1LYSGLUE186 - 191
d_514ens_1SERLYSE199 - 205
d_515ens_1SERASNE207 - 214
d_516ens_1GLYILEE216 - 230
d_61ens_1METMETF2
d_62ens_1LEUILEF4 - 19
d_63ens_1GLNGLNF21 - 36
d_64ens_1VALSERF38 - 71
d_65ens_1LEUASNF74 - 90
d_66ens_1ARGASNF92 - 105
d_67ens_1THRGLYF107 - 120
d_68ens_1LYSHISF122 - 131
d_69ens_1TRPVALF134 - 157
d_610ens_1VALGLUF159 - 160
d_611ens_1TRPARGF162 - 163
d_612ens_1ASNASPF165 - 177
d_613ens_1LYSGLUF180 - 185
d_614ens_1SERLYSF189 - 195
d_615ens_1SERASNF197 - 204
d_616ens_1GLYILEF206 - 220
d_71ens_1METMETG2
d_72ens_1LEUILEG4 - 19
d_73ens_1GLNGLNG21 - 36
d_74ens_1VALSERG38 - 71
d_75ens_1LEUASNG76 - 92
d_76ens_1ARGASNG94 - 107
d_77ens_1THRGLYG109 - 122
d_78ens_1LYSHISG124 - 133
d_79ens_1TRPVALG140 - 163
d_710ens_1VALGLUG165 - 166
d_711ens_1TRPARGG168 - 169
d_712ens_1ASNASPG171 - 183
d_713ens_1LYSGLUG186 - 191
d_714ens_1SERLYSG195 - 201
d_715ens_1SERASNG203 - 210
d_716ens_1GLYILEG212 - 226
d_81ens_1METMETH2
d_82ens_1LEUILEH4 - 19
d_83ens_1GLNGLNH21 - 36
d_84ens_1VALSERH38 - 71
d_85ens_1LEUASNH76 - 92
d_86ens_1ARGASNH94 - 107
d_87ens_1THRGLYH109 - 122
d_88ens_1LYSHISH124 - 133
d_89ens_1TRPVALH140 - 163
d_810ens_1VALGLUH165 - 166
d_811ens_1TRPARGH168 - 169
d_812ens_1ASNASPH171 - 183
d_813ens_1LYSGLUH186 - 191
d_814ens_1SERLYSH199 - 205
d_815ens_1SERASNH207 - 214
d_816ens_1GLYILEH216 - 230
d_91ens_1METMETI1
d_92ens_1LEUILEI3 - 18
d_93ens_1GLNGLNI20 - 35
d_94ens_1VALSERI37 - 70
d_95ens_1LEUASNI75 - 91
d_96ens_1ARGASNI93 - 106
d_97ens_1THRGLYI108 - 121
d_98ens_1LYSHISI123 - 132
d_99ens_1TRPVALI139 - 162
d_910ens_1VALGLUI164 - 165
d_911ens_1TRPARGI167 - 168
d_912ens_1ASNASPI170 - 182
d_913ens_1LYSGLUI185 - 190
d_914ens_1SERLYSI198 - 204
d_915ens_1SERASNI206 - 213
d_916ens_1GLYILEI215 - 229
d_101ens_1METMETJ2
d_102ens_1LEUILEJ4 - 19
d_103ens_1GLNGLNJ21 - 36
d_104ens_1VALSERJ38 - 71
d_105ens_1LEUASNJ76 - 92
d_106ens_1ARGASNJ94 - 107
d_107ens_1THRGLYJ109 - 122
d_108ens_1LYSHISJ124 - 133
d_109ens_1TRPVALJ138 - 161
d_1010ens_1VALGLUJ163 - 164
d_1011ens_1TRPARGJ166 - 167
d_1012ens_1ASNASPJ169 - 181
d_1013ens_1LYSGLUJ184 - 189
d_1014ens_1SERLYSJ200 - 206
d_1015ens_1SERASNJ208 - 215
d_1016ens_1GLYILEJ217 - 231
d_111ens_1METMETK2
d_112ens_1LEUILEK4 - 19
d_113ens_1GLNGLNK21 - 36
d_114ens_1VALASNK38 - 88
d_115ens_1ARGASNK90 - 103
d_116ens_1THRGLYK105 - 118
d_117ens_1LYSHISK120 - 129
d_118ens_1TRPVALK136 - 159
d_119ens_1VALGLUK161 - 162
d_1110ens_1TRPARGK164 - 165
d_1111ens_1ASNASPK167 - 179
d_1112ens_1LYSGLUK182 - 187
d_1113ens_1SERLYSK192 - 198
d_1114ens_1SERASNK200 - 207
d_1115ens_1GLYILEK209 - 223
d_121ens_1METMETL2
d_122ens_1LEUILEL4 - 19
d_123ens_1GLNGLNL21 - 36
d_124ens_1VALSERL38 - 71
d_125ens_1LEUASNL76 - 92
d_126ens_1ARGASNL94 - 107
d_127ens_1THRGLYL109 - 122
d_128ens_1LYSHISL124 - 133
d_129ens_1TRPVALL138 - 161
d_1210ens_1VALGLUL163 - 164
d_1211ens_1TRPARGL166 - 167
d_1212ens_1ASNASPL169 - 181
d_1213ens_1LYSGLUL184 - 189
d_1214ens_1SERLYSL192 - 198
d_1215ens_1SERASNL200 - 207
d_1216ens_1GLYILEL209 - 223
d_131ens_1METMETM2
d_132ens_1LEUILEM4 - 19
d_133ens_1GLNGLNM21 - 36
d_134ens_1VALSERM38 - 71
d_135ens_1LEUASNM76 - 92
d_136ens_1ARGASNM94 - 107
d_137ens_1THRGLYM109 - 122
d_138ens_1LYSHISM124 - 133
d_139ens_1TRPVALM140 - 163
d_1310ens_1VALGLUM165 - 166
d_1311ens_1TRPARGM168 - 169
d_1312ens_1ASNASPM171 - 183
d_1313ens_1LYSGLUM186 - 191
d_1314ens_1SERLYSM195 - 201
d_1315ens_1SERASNM203 - 210
d_1316ens_1GLYILEM212 - 226
d_141ens_1METMETN2
d_142ens_1LEUILEN4 - 19
d_143ens_1GLNGLNN21 - 36
d_144ens_1VALSERN38 - 71
d_145ens_1LEUASNN76 - 92
d_146ens_1ARGASNN94 - 107
d_147ens_1THRGLYN109 - 122
d_148ens_1LYSHISN124 - 133
d_149ens_1TRPVALN135 - 158
d_1410ens_1VALGLUN160 - 161
d_1411ens_1TRPARGN163 - 164
d_1412ens_1ASNASPN166 - 178
d_1413ens_1LYSGLUN181 - 186
d_1414ens_1SERLYSN193 - 199
d_1415ens_1SERASNN201 - 208
d_1416ens_1GLYILEN210 - 224
d_151ens_1METMETO2
d_152ens_1LEUILEO4 - 19
d_153ens_1GLNGLNO21 - 36
d_154ens_1VALSERO38 - 71
d_155ens_1LEUASNO76 - 92
d_156ens_1ARGASNO94 - 107
d_157ens_1THRGLYO109 - 122
d_158ens_1LYSHISO124 - 133
d_159ens_1TRPVALO140 - 163
d_1510ens_1VALGLUO165 - 166
d_1511ens_1TRPARGO168 - 169
d_1512ens_1ASNASPO171 - 183
d_1513ens_1LYSGLUO186 - 191
d_1514ens_1SERLYSO194 - 200
d_1515ens_1SERASNO202 - 209
d_1516ens_1GLYILEO211 - 225
d_161ens_1METMETP2
d_162ens_1LEUILEP4 - 19
d_163ens_1GLNGLNP21 - 36
d_164ens_1VALSERP38 - 71
d_165ens_1LEUASNP76 - 92
d_166ens_1ARGASNP94 - 107
d_167ens_1THRGLYP109 - 122
d_168ens_1LYSHISP124 - 133
d_169ens_1TRPVALP140 - 163
d_1610ens_1VALGLUP165 - 166
d_1611ens_1TRPARGP168 - 169
d_1612ens_1ASNASPP171 - 183
d_1613ens_1LYSGLUP186 - 191
d_1614ens_1SERLYSP196 - 202
d_1615ens_1SERASNP204 - 211
d_1616ens_1GLYILEP213 - 227

NCS oper:
IDCodeMatrixベクター
1given(-0.163635064106, 0.986296107708, 0.0210607149603), (0.986114977123, 0.162918059882, 0.0321707578013), (0.0282987223804, 0.0260325504665, -0.999260470862)76.9113362789, -65.3306279307, 3.17467615569
2given(-0.253570555199, -0.642381379153, 0.723220669819), (-0.673880257401, -0.419067325327, -0.608496487688), (0.693964964693, -0.641660923355, -0.326624994785)-50.9865723635, -56.2639520449, 0.0233702533531
3given(-0.599989015954, -0.315302134777, -0.73525352399), (-0.34242613514, -0.729396496558, 0.592220476497), (-0.723019724978, 0.607095803489, 0.329662194797)-24.7949676449, -81.0015338409, 94.8797471567
4given(-0.996198041844, 0.0821652079867, -0.0289541019979), (0.0763149877192, 0.662762861922, -0.744930474277), (-0.04201766385, -0.744307911723, -0.666513502092)17.6064217156, -9.75204757186, -19.6660561785
5given(0.202989683176, -0.979166542398, -0.00529818571803), (0.64852550388, 0.130387064847, 0.749942587227), (-0.733627875248, -0.155666616744, 0.661481704275)-63.5817021311, -51.5901351514, 24.3680809096
6given(0.237062127446, 0.6306376859, -0.738984206092), (-0.971406049282, 0.164136781498, -0.171550005476), (0.0131085906959, 0.758521737383, 0.651515877602)9.55482852412, -6.29636798714, 117.654424221
7given(0.592778811574, 0.288758790634, 0.751818888683), (0.284953232362, -0.948327341071, 0.139559698856), (0.753269497534, 0.131505190049, -0.644431104987)-17.6796274765, -91.7524640975, 70.4923747771
8given(-0.268191824423, -0.639423261001, 0.720563001134), (-0.638437381753, -0.442159283883, -0.629994347004), (0.721436660347, -0.628993689131, -0.289648207555)-16.8777913339, -72.7270102832, -47.3709115835
9given(-0.570691628256, -0.344791074526, -0.745271883521), (-0.346432017189, -0.721767109584, 0.599197043541), (-0.744510525718, 0.600142778387, 0.292459779533)6.8617783495, -95.2269356509, 48.1435323583
10given(0.189779692988, -0.981819444689, -0.00377440860404), (0.628626068569, 0.118554774555, 0.768618261132), (-0.754196880161, -0.148240829264, 0.639696586277)-84.0490735963, -23.4994300268, 71.72676816
11given(-0.997929378408, 0.0643146213437, 0.000764978190126), (0.0422631033881, 0.664642637484, -0.745965142973), (-0.0484849028278, -0.744388201088, -0.665984549579)-3.87641627578, 19.3508805503, 26.926083775
12given(0.573090943771, 0.278777106686, 0.770616697818), (0.263020107704, -0.953181057053, 0.149218951269), (0.776136066107, 0.117171657247, -0.619583416197)14.8653963564, -106.088056213, 23.3261497534
13given(0.205985081211, 0.631052986939, -0.747891886568), (-0.97831045826, 0.149892953365, -0.142971150206), (0.0218813522919, 0.761120378263, 0.64824144901)42.8887038846, -21.4815068967, 71.679130568
14given(0.999395399703, -0.0191965976227, -0.0289883716632), (0.0198641549918, 0.999539966252, 0.0229187960471), (0.0285350731282, -0.0234807688439, 0.999316968282)-21.6625622758, 28.6996619804, 45.8901304941
15given(-0.138927220776, 0.98953641669, 0.0389474950563), (0.99023480691, 0.139270392516, -0.00622775665907), (-0.0115868249324, 0.0377019603223, -0.99922185108)55.3770634448, -37.0315852086, 52.3207837577

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要素

#1: タンパク質
Poxin / Protein p26 / p26


分子量: 27399.492 Da / 分子数: 16 / 由来タイプ: 組換発現
由来: (組換発現) Autographa californica nuclear polyhedrosis virus (ウイルス)
遺伝子: P26 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: P08358, 加水分解酵素; エステル加水分解酵素
#2: 化合物
ChemComp-9BG / 2',5'-GpAp / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate


分子量: 692.427 Da / 分子数: 16 / 由来タイプ: 合成 / 式: C20H26N10O14P2 / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3334 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.42 Å3/Da / 溶媒含有率: 63.99 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 100 mM sodium acetate, 35-39% PEG-400 / PH範囲: 4.8 - 5.2

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9793 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2018年12月6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: 0.9793 Å / 相対比: 1
反射解像度: 1.9→38.31 Å / Num. obs: 422103 / % possible obs: 92.3 % / 冗長度: 3.7 % / CC1/2: 0.994 / Rpim(I) all: 0.045 / Net I/σ(I): 19.5
反射 シェル解像度: 1.9→1.93 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 20247 / CC1/2: 0.623 / Rpim(I) all: 0.581 / % possible all: 90

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
XDSデータ削減
Aimlessデータスケーリング
AutoSol位相決定
精密化構造決定の手法: 分子置換
開始モデル: Unpublished SAD-phased structure of a Se-Met derivative

解像度: 1.9→38.31 Å / 交差検証法: FREE R-VALUE / σ(F): 25.45 / 位相誤差: 22.5078
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
詳細: Twin Law: -l,-h,h+k+l
Rfactor反射数%反射
Rfree0.2083 2037 1.15 %
Rwork0.1748 417174 -
obs0.1864 422034 92.33 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 28.29 Å2
精密化ステップサイクル: LAST / 解像度: 1.9→38.31 Å
タンパク質核酸リガンド溶媒全体
原子数29078 0 736 3334 33148
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00730519
X-RAY DIFFRACTIONf_angle_d1.012941536
X-RAY DIFFRACTIONf_chiral_restr0.06124741
X-RAY DIFFRACTIONf_plane_restr0.00655171
X-RAY DIFFRACTIONf_dihedral_angle_d16.428411064
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.563630497636
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.734336008771
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.687472902132
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.726509881854
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.510216792048
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.682585902744
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.585097641526
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.546416319108
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS0.407304821799
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS0.689300059488
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS0.566369646369
ens_1d_13AX-RAY DIFFRACTIONTorsion NCS0.729519099116
ens_1d_14AX-RAY DIFFRACTIONTorsion NCS0.539188426111
ens_1d_15AX-RAY DIFFRACTIONTorsion NCS0.684630162686
ens_1d_16AX-RAY DIFFRACTIONTorsion NCS0.686104458665
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.28381220.278927337X-RAY DIFFRACTION89.97
1.94-1.990.2931380.261827460X-RAY DIFFRACTION90.16
1.99-2.050.29981310.243127417X-RAY DIFFRACTION89.87
2.05-2.110.30451460.226628663X-RAY DIFFRACTION93.84
2.11-2.170.27221390.222428423X-RAY DIFFRACTION93.54
2.17-2.250.19531360.215628429X-RAY DIFFRACTION93
2.25-2.340.23621350.209427816X-RAY DIFFRACTION91.7
2.34-2.450.22891350.206826819X-RAY DIFFRACTION87.52
2.45-2.580.23571470.200728651X-RAY DIFFRACTION94.54
2.58-2.740.1921400.191928735X-RAY DIFFRACTION94.12
2.74-2.950.23921260.193928339X-RAY DIFFRACTION92.65
2.95-3.250.25991290.182126760X-RAY DIFFRACTION88.25
3.25-3.720.19651420.176529067X-RAY DIFFRACTION95.06
3.72-4.680.17321300.150827417X-RAY DIFFRACTION90.01
4.68-38.310.17881410.154728664X-RAY DIFFRACTION94.02
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6428815902060.2564208789860.02882005377961.110053421010.002714201837260.164581708425-0.1197484977250.1123702489760.162768129377-0.1789164455940.0269692682954-0.0917531197942-0.189901077861-0.1506728434580.06411518951870.2618664411770.00510032754592-0.03056843172450.1713239823170.0522920459430.34937257281814.8488399575-13.7347913992-6.0096955305
21.40699443297-0.395941842222-0.1542326201051.19720445146-0.1781752847740.977875043757-0.0992901459907-0.1253035808360.102228665713-0.1184719077050.0266476147363-0.00932754244146-0.071046452639-0.07430855526770.04609958822870.172221635858-0.0167946487382-0.01267415215450.1524389644440.007054109064070.20319708016819.7667909976-27.4111764407-3.09877491117
30.973089077307-0.331390626951-0.3351004111841.520681707460.2041212211590.851704718618-0.00657050264865-0.03803247678310.3333170591080.2086196949820.0510798182948-0.0424908874719-0.1487784358890.1062545466680.01735559525950.166282513991-0.00283198382132-0.04604807797680.165845351390.0182580647990.26819987793626.9225797873-21.6024900472.91860616246
41.584362578870.05387450520740.6005926300981.25749213404-0.3934310901541.41884144394-0.0838720644947-0.3135548696020.385747261360.0933516841729-0.0281238951895-0.163744299293-0.258781927503-0.1443066101410.02279104523180.221299839308-0.00018473257852-0.03927069147940.202014420496-0.05809872013640.36016811210724.5445662563-11.25514638184.49847219137
51.33381578232-0.2778894684850.1896826486171.78718791756-0.03967460427051.7909339228-0.366530425738-0.2378949073610.2613354077620.391963511705-0.0656110124745-0.143345376789-0.146608627784-0.4734417784510.4572211008620.258895411837-0.000699362938518-0.06634443579890.149812147595-0.0256909627980.29379576116827.2450667477-17.79025272067.52817957633
60.709028251571-0.5140746501070.2886731293251.147332686530.3397733389150.983729671137-0.0212930423455-0.04571330216550.0885688804049-0.009523002857310.0679122657825-0.204121294570.01759250437020.0550913573808-0.07901403661660.1624336097450.00172422784616-0.03524359891920.158326382828-0.009475051584760.22214924180426.9152665685-31.37530846411.80011027605
71.730874100310.05452319144480.6222296608820.5872963498210.002890639417182.154280244630.0663673679406-0.408368046427-0.1548602639670.1231347497830.03223647695320.04511104935110.0719226801536-0.165900698995-0.09132651519640.23028753437-0.041672496991-0.01934012285990.2354435880760.02143302921970.17876593502431.6796621296-47.519970616218.3211652341
80.645815499711-0.3951406805620.3266885422080.467677629545-0.336995710330.498163859535-0.0625402812217-0.1165228158090.0123839510038-0.02893969903530.09741683699080.05576837511560.0297407002842-0.0628316152867-0.0005941106019150.178569064429-0.00561454136902-0.02332761485850.1946574761710.008612867324190.19454792930226.8919287285-44.706911159610.3314074921
90.3924571385670.0599593643513-0.5876658095030.9121098437550.3982887579061.14979370793-0.014777292182-0.09125758875760.128599225573-0.0116350680995-0.0860003198437-0.08092708741060.01191695796840.3009376201910.1578209010750.18129365827-0.00731341488002-0.08410987534330.3064320288780.0003556561189330.37414210723662.8546388912-52.53885949917.71651085285
100.998146145345-0.0715040660623-0.2114051457560.848831684247-0.1409667477740.6874278271050.0870328218675-0.0267232918531-0.1120337698670.00262988808913-0.0130756208197-0.02222466514420.227797954250.138442761874-0.02804951563870.176163846242-0.0145706011095-0.04481660413680.177146318054-0.01334496261510.23834356475549.9082385319-55.66155352635.12099750106
111.2191998108-0.58781223693-0.002087988028950.545448463128-0.1826584999921.170675230980.046009122890.08041769789130.1035018546120.0438941195362-0.0512877645196-0.163926365383-0.0821972246720.0922965392748-0.02661362783590.147108869641-0.0172415134175-0.04113154864480.160122282943-0.003616938601560.23921572777949.7005821038-44.4416317413.90828513088
121.95291418548-0.544957473166-0.2044683477821.40456550175-0.3000843524871.607737635160.1686287493720.2698096583690.217305179342-0.0634739564242-0.128833014719-0.198315006391-0.1383292336540.2583489027640.006126736337150.151527410933-0.0173349759650.001604302125420.2464951884750.03096687197380.30402059516557.9676372625-41.7779161121-2.69264319182
131.44276788416-0.332700061417-0.2153397406221.147182936130.08582963400951.704117588560.1255544092720.06069362624590.03835922805590.0899018245243-0.0183193995428-0.133628110495-0.0619497544044-0.0585797383607-0.06581217792450.1336542324690.0227958663465-0.00995681513960.1686352732280.01556167313920.19982858533837.8779718505-44.97596399983.17021823193
141.08097560452-0.3918438207010.1681111459421.23509123024-0.7097446728871.08528852189-0.01177065339750.305708309411-0.100415182356-0.4700187621570.0662874342122-0.1480626996140.188640556830.22934638389-0.07361262744770.235374662101-0.02610255594740.01168722068860.219835031104-0.01204351095790.15962943031929.6365343425-42.4477975344-15.8546170488
150.3441079727860.0730490588805-0.09808234118461.89985529106-0.4549520894670.643009573972-0.00877232548513-0.0431217547021-0.102378303839-0.2974097537180.08240874559770.2763872726450.079781647498-0.143671470863-0.002437867366970.248344870763-0.0229339751044-0.06268406996450.2259176013680.03011631118110.25571567170423.7736898685-44.1543950827-11.5297109238
161.527477746990.236581657870.1769370896291.52183224426-0.7498294122040.852740593537-0.0120367291179-0.0808874231154-0.00343044698683-0.0928127325953-0.0423627943251-0.05026764847490.0437768035868-0.06810654401170.03703445491430.168015673469-0.0198392145542-0.003008226608140.161939808307-0.02222864124980.17196804918730.0101209997-43.3208323182-5.93731897069
171.521393104420.304968052209-0.6716324852591.733464868340.259909820251.843813872840.197172180128-0.273333630168-0.125016378954-0.123360655201-0.2057996446930.2853144876580.114397303911-0.2038046528550.004674230478650.225355384925-0.0255510126763-0.08427288625070.2992100914660.01957327453120.303230596056-50.3268515419-58.910400806919.142243738
181.09311625601-0.413667861556-0.019260967790.689999529428-0.3456038414631.179153721650.082839347690.054940138112-0.004313244836110.0027946428767-0.125345987175-0.00545378856012-0.0786024245902-0.002785641332860.06496801580190.187038289486-0.0251854435947-0.0031345711880.25762873362-0.00656474184210.257415330218-40.2100066802-53.804445262326.5485886223
190.895537746528-0.1568510329410.2207984965370.5566102665950.3747115942911.208704507820.0551649133501-0.0867006435569-0.120834647072-0.110503615959-0.01248861873120.2379824056530.139120465881-0.147008078337-0.08257334616860.212120541808-0.0495312935092-0.03962954493450.2624712676780.04304316144640.247013086794-43.9252187882-62.447575512131.9678595074
201.58698542269-0.3228004615070.4967680016360.7721033430720.2188125076511.235214348510.04020196319860.102349424948-0.312470536761-0.04692697603590.07302472647670.2451743243270.191223830716-0.0490107282138-0.0845295444640.249754348944-0.0418284434346-0.02856576196070.2384294307210.02124898099730.284471133752-44.2611367383-67.629561970628.4781349079
210.927221596253-0.1650514365070.3072749422120.7170504062480.01183596512971.161385456140.0442602570945-0.0777972109137-0.1368821458940.01837256531930.04080976929070.1165979950140.320141201190.0886179533024-0.09817247642050.262957463061-0.00768743787409-0.04493097471390.2270560165530.006740375742090.191170094226-36.3819107177-66.620823602134.6833410003
221.74847250654-0.1590781677450.8106939672980.533858529123-0.2807158739912.545260449120.00157258063620.482619239746-0.132320328403-0.250559711775-0.0461768070438-0.3344919838710.3700315732310.3974284745550.07086204654910.225410040910.01190313837070.01219645962430.3784376549-0.02036658406910.269523926051-17.3182965292-69.87327596542.3340052634
230.972662702387-0.2384792086070.3393908913141.018195339450.07836607971050.826806980087-0.133956247681-0.00306535382966-0.0965234758299-0.09000684133980.0542422729159-0.2429438979050.05228585886180.3870863604850.01814566467040.2479969611320.0182986597550.0003853637193460.4429727856650.04441068109640.304215451082-16.9548331188-66.222311283546.5955351164
241.118819938110.05539579172050.3847505267991.16441685525-0.05355641422530.903077373967-0.04924674198580.142179888675-0.0712945526018-0.0754781079290.0864866195142-0.09422572548410.0005716142569040.406954791788-0.03952468746490.226862972014-0.0248037772899-0.01195805465240.2862284072690.01039796470560.197163524313-24.5853773787-63.601858607544.1673017509
250.6882932088120.430267414769-0.09757495354291.409484387331.188782390091.457613865540.0471820255646-0.22307609249-0.24420605339-0.001652144874420.1120449446890.06189590978070.297998419203-0.253002438845-0.1730086312910.31604629421-0.0380572698946-0.06100974658390.2211077561410.07302470464750.260400695235-27.0705594718-80.149401750275.6850749821
260.755813866929-0.04125292836190.1857745685660.5095522683440.09649345034951.0623357378-0.128210646702-0.03690666521060.0106394889952-0.05542229110660.0547440899341-0.07146395170790.08141716356340.04426669210840.04516833817410.284430070131-0.0324805977314-0.007970356899340.197791065967-0.01095530180730.278094362948-23.601821828-68.996589899668.8005389304
271.14604038550.02438242690610.08349826253411.080458975250.2353329494761.70504389976-0.0538464921971-0.112228091503-0.202919625199-0.1115210451160.111995463906-0.06786785703760.08757335290420.0135127116556-0.09760475831480.283284029723-0.0411301261131-0.01407255457560.1820498568590.03040198291880.224404807932-25.2808786701-73.165689357260.8124521458
280.8866168316950.199737622721-0.09315843632261.23799615151-0.1870763757071.347612615350.175094372141-0.128195762297-0.1037231429570.2479213375-0.01341395494270.2661638676090.0538771187441-0.291403199726-0.08962962736510.275929969872-0.0440867471689-0.02440748949290.3022690193190.0520790605980.280415643768-36.7989782287-74.777976450664.8936641153
290.9021609514521.0220071028-0.1606522283332.50100681555-0.4452001832292.20795576130.131854248546-0.06943855839440.0849715329776-0.0748874194148-0.03285269477290.275500053969-0.171418269413-0.176651401715-0.1178469566230.2210962394220.0130501204963-0.03708138387810.2258532045130.02563443737520.20631657138-34.6717305105-67.90133726358.7021769195
301.914770451420.3953925091670.5677245372511.714877128150.08245658753911.89711715233-0.257204611808-0.272947738346-0.2044363186550.2461088004480.2881836550110.3959797691840.433475062016-0.447924049562-0.00944778914420.305849210373-0.0694203737525-0.02898972780130.3350559653670.07575698701770.288836847897-38.6287877705-79.039590513171.385377688
310.5776174806580.2808299155890.7597775721481.57871258049-0.7664770162061.9680770351-0.0231645717784-0.195726569645-0.0784777257335-0.008123306064390.3127805187680.305999570364-0.119485943599-0.388990125408-0.2020728623340.214856946802-0.0614193381201-0.03773704635490.3220307141210.09258439962940.252694275506-42.0213910565-71.729276553366.599010007
320.617557146517-0.4666380177530.3342584770471.26508196845-0.3592053714931.87403680960.05062224286270.0824172019774-0.08319202984360.228555516823-0.0183921973591-0.13984520552-0.0556602694749-0.1666884185050.01640268231310.2224265813580.00196559138118-0.008130970566790.2306657717110.03658237769280.227379580603-29.2966966559-64.491635905354.2654751385
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1230.2722346210170.9120263874170.7812001558053.288898717732.87510988462.52439676596-0.183200917223-0.1325160001160.3783961310190.5261845695180.0606070374214-0.0735874917754-0.194710728993-0.0505645345989-0.1599759219040.3729174710320.0560231622267-0.09258668413110.355213494041-0.05169868045430.3471514690441.7974054110218.419289458456.383313268
1240.5264208678411.0476301946-0.1306481799613.02289878467-0.3314443605660.0629032752972-0.09865013948510.5292400270070.130134544477-0.290066856580.0255729093247-0.5113146858840.007261151242060.007490058028420.09677166796050.244222503708-0.0592992573459-0.01241592844930.2553445153650.02894394762140.3783874367344.9607876049715.003911003440.3807327897
1250.7211295788620.6158640077191.392702432340.5335348566131.23663902652.90939552395-0.287004550165-0.3394748302910.5254191184070.708744076849-0.0847639835814-0.1776316190420.0249605380847-0.01823848648760.08377028857880.3985636735940.0565623617373-0.1322554822380.323930388075-0.06124385579010.4138059470486.3843683120411.156727657660.765481898
1261.14052440559-0.377932973739-0.1009634746850.9478822102880.151283934830.885578837723-0.160751265595-0.03461974228390.0587447444461-0.1001616697690.160434856449-0.1436030818540.04489457160820.105933703473-0.02917811150390.1905191383820.0232209624064-0.01602486024180.1961037425920.02291266546130.2607453717645.83164515981-2.2579948659949.0341137043
1270.67200948049-0.367230132032-1.105908902491.435975296790.6476635505142.40255689121-0.0154457072194-0.593540432889-0.04049005655990.5345328579270.2370437935750.208284351007-0.0541329327758-0.0791791747129-0.195791329030.3552797420430.0242020686640.03435950415660.3064869879050.04027743583130.2486033328088.60124243486-13.304206413566.5351305844
1280.346885197237-0.6152260758640.1754359520381.53209398619-0.8967582138160.952326649473-0.119560708056-0.351607616386-0.2442291415290.5825459631780.1262168550350.179470518410.0548393437820.1643887685560.02051922908390.3498748186590.08564675350970.0117824298510.3508790395090.103639806870.364403893889.79079008095-17.710957285763.4473850604
1290.241959719291-0.05731321647910.1600188206710.0194486108669-0.05101437328330.122026709274-0.101913815267-0.0563939612513-0.09091272489770.1229729479510.09497411380010.104838219603-0.0776555496698-0.164419687061-0.02869542727390.2298095030050.03076168552980.01566076948550.2719492125210.0172973747080.3018366382947.48114529589-12.306940892457.0155461585
1300.9602792013840.235190138987-0.05939787836581.93268028681.330913042492.08940672165-0.0613200852740.02146004628850.2418232305230.0785782425351-0.00779726609355-0.155401655154-0.0596944035810.514170440420.1642507659320.248917237073-0.0160457646674-0.07740963890480.3104306474920.03705536616680.35126055990342.9566645678-23.550796569855.005319508
1311.69512376147-0.363338060076-0.1713416454461.56158078418-0.6321208547370.51980465338-0.063396943944-0.22029298650.3165786219060.290923890218-0.0871835839549-0.02585783154970.3111732028020.1285179265890.2636059074350.239620976649-0.00183737555977-0.04180823286790.261414740845-0.03372389273610.28969143426135.9070502769-25.107564305859.8714854799
1320.923862087726-0.0341303284868-0.0414671126011.446681231430.2671268562831.81197538537-0.130385109093-0.000939349913206-0.0222996963953-0.05441776771420.0007417725254730.1234142567750.280349500746-0.04512132116320.1655640502420.18367216385-0.0118306499125-0.03151656717450.183237836642-0.0285810471590.22230216387223.4889098337-26.493636450352.8859841188
1331.21926262657-0.643135245587-0.1326428918920.4882978470020.1166255261110.9792483403040.06327412820820.01123164410280.1534987112850.0551620147119-0.115169215819-0.208460164987-0.1971993701140.06918395024780.01948468831280.248339042811-0.0230974315191-0.04215986135120.2140432854860.01494789101950.30641013816230.0141624134-12.636514165750.4447318712
1341.0126590001-0.217382772227-0.6852978293240.355541090009-0.02130593151470.9124812053340.08227221574720.3575684919130.243726478144-0.047488915093-0.0714246951291-0.225162687702-0.206530883880.324339611111-0.01094669026310.226280059759-0.0271524192546-0.01463811829750.3273603486850.0530106326870.37354019170736.9823254167-13.273947094845.0834827825
1351.85892567024-0.3144834941880.3265103849051.069886717310.04287962812561.559295767320.236220650557-0.0983971870403-0.04986957963490.113536789683-0.0835212115589-0.141219575042-0.0709007517042-0.1759204696630.0127396062960.1828242329360.01823817893670.003864233817760.2350135086360.004195909376060.22374944408316.7577508791-15.730106352551.0664339697
1360.7372897179230.60399057072-0.09401720215950.599944908219-0.04909208719350.5355436340580.03519907133320.270836851792-0.200237215374-0.4910800559170.02301909286870.1134483449950.12865589898-0.0139216174882-5.18036579958E-60.3131821502310.0361456477789-0.07558432964040.330349911068-0.04702637952120.2919248744935.79360187676-14.381747751233.3745022027
1370.599219919122-0.5602041769970.04438614749220.674686230344-0.2084326758970.178855229380.07875597123610.120159880858-0.00355203332572-0.115636190395-0.1288907730410.00483236330864-0.0121089562971-0.04797029865270.03386708327570.2075464057720.0111966986572-0.008864602946920.217492231912-0.01051926469570.25275944759811.0431785993-13.608256791840.6016517241
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 30 )AA0 - 301 - 31
22chain 'A' and (resid 31 through 64 )AA31 - 6432 - 65
33chain 'A' and (resid 65 through 104 )AA65 - 10466 - 105
44chain 'A' and (resid 105 through 122 )AA105 - 122106 - 123
55chain 'A' and (resid 123 through 138 )AA123 - 138124 - 139
66chain 'A' and (resid 139 through 162 )AA139 - 162140 - 163
77chain 'A' and (resid 163 through 190 )AA163 - 190164 - 191
88chain 'A' and (resid 191 through 233 )AA191 - 233192 - 234
99chain 'B' and (resid 1 through 21 )BB1 - 211 - 21
1010chain 'B' and (resid 22 through 39 )BB22 - 3922 - 39
1111chain 'B' and (resid 40 through 104 )BB40 - 10440 - 104
1212chain 'B' and (resid 105 through 143 )BB105 - 143105 - 143
1313chain 'B' and (resid 144 through 162 )BB144 - 162144 - 162
1414chain 'B' and (resid 163 through 180 )BB163 - 180163 - 180
1515chain 'B' and (resid 181 through 209 )BB181 - 209181 - 206
1616chain 'B' and (resid 210 through 232 )BB210 - 232207 - 229
1717chain 'C' and (resid 1 through 21 )CC1 - 211 - 21
1818chain 'C' and (resid 22 through 39 )CC22 - 3922 - 39
1919chain 'C' and (resid 40 through 92 )CC40 - 9240 - 92
2020chain 'C' and (resid 93 through 127 )CC93 - 12793 - 127
2121chain 'C' and (resid 128 through 162 )CC128 - 162128 - 162
2222chain 'C' and (resid 163 through 180 )CC163 - 180163 - 180
2323chain 'C' and (resid 181 through 209 )CC181 - 209181 - 202
2424chain 'C' and (resid 210 through 233 )CC210 - 233203 - 226
2525chain 'D' and (resid 1 through 21 )DD1 - 211 - 21
2626chain 'D' and (resid 22 through 39 )DD22 - 3922 - 39
2727chain 'D' and (resid 40 through 64 )DD40 - 6440 - 64
2828chain 'D' and (resid 65 through 92 )DD65 - 9265 - 92
2929chain 'D' and (resid 93 through 104 )DD93 - 10493 - 104
3030chain 'D' and (resid 105 through 123 )DD105 - 123105 - 123
3131chain 'D' and (resid 124 through 143 )DD124 - 143124 - 143
3232chain 'D' and (resid 144 through 162 )DD144 - 162144 - 162
3333chain 'D' and (resid 163 through 209 )DD163 - 209163 - 201
3434chain 'D' and (resid 210 through 233 )DD210 - 233202 - 225
3535chain 'E' and (resid 0 through 15 )EE0 - 151 - 16
3636chain 'E' and (resid 16 through 64 )EE16 - 6417 - 65
3737chain 'E' and (resid 65 through 143 )EE65 - 14366 - 144
3838chain 'E' and (resid 144 through 162 )EE144 - 162145 - 163
3939chain 'E' and (resid 163 through 180 )EE163 - 180164 - 181
4040chain 'E' and (resid 181 through 209 )EE181 - 209182 - 207
4141chain 'E' and (resid 210 through 233 )EE210 - 233208 - 231
4242chain 'F' and (resid 0 through 15 )FF0 - 151 - 16
4343chain 'F' and (resid 16 through 104 )FF16 - 10417 - 103
4444chain 'F' and (resid 105 through 122 )FF105 - 122104 - 121
4545chain 'F' and (resid 123 through 138 )FF123 - 138122 - 133
4646chain 'F' and (resid 139 through 162 )FF139 - 162134 - 157
4747chain 'F' and (resid 163 through 180 )FF163 - 180158 - 175
4848chain 'F' and (resid 181 through 219 )FF181 - 219176 - 207
4949chain 'F' and (resid 220 through 232 )FF220 - 232208 - 220
5050chain 'G' and (resid 0 through 15 )GG0 - 151 - 16
5151chain 'G' and (resid 16 through 30 )GG16 - 3017 - 31
5252chain 'G' and (resid 31 through 104 )GG31 - 10432 - 105
5353chain 'G' and (resid 105 through 122 )GG105 - 122106 - 123
5454chain 'G' and (resid 123 through 138 )GG123 - 138124 - 139
5555chain 'G' and (resid 139 through 162 )GG139 - 162140 - 163
5656chain 'G' and (resid 163 through 180 )GG163 - 180164 - 181
5757chain 'G' and (resid 181 through 209 )GG181 - 209182 - 203
5858chain 'G' and (resid 210 through 232 )GG210 - 232204 - 226
5959chain 'H' and (resid 0 through 30 )HH0 - 301 - 31
6060chain 'H' and (resid 31 through 64 )HH31 - 6432 - 65
6161chain 'H' and (resid 65 through 81 )HH65 - 8166 - 82
6262chain 'H' and (resid 82 through 104 )HH82 - 10483 - 105
6363chain 'H' and (resid 105 through 122 )HH105 - 122106 - 123
6464chain 'H' and (resid 123 through 138 )HH123 - 138124 - 139
6565chain 'H' and (resid 139 through 162 )HH139 - 162140 - 163
6666chain 'H' and (resid 163 through 209 )HH163 - 209164 - 207
6767chain 'H' and (resid 210 through 234 )HH210 - 234208 - 232
6868chain 'I' and (resid 1 through 21 )II1 - 211 - 21
6969chain 'I' and (resid 22 through 39 )II22 - 3922 - 39
7070chain 'I' and (resid 40 through 104 )II40 - 10440 - 104
7171chain 'I' and (resid 105 through 122 )II105 - 122105 - 122
7272chain 'I' and (resid 123 through 162 )II123 - 162123 - 162
7373chain 'I' and (resid 163 through 180 )II163 - 180163 - 180
7474chain 'I' and (resid 181 through 209 )II181 - 209181 - 206
7575chain 'I' and (resid 210 through 232 )II210 - 232207 - 229
7676chain 'J' and (resid 0 through 15 )JJ0 - 151 - 16
7777chain 'J' and (resid 16 through 30 )JJ16 - 3017 - 31
7878chain 'J' and (resid 31 through 53 )JJ31 - 5332 - 54
7979chain 'J' and (resid 54 through 104 )JJ54 - 10455 - 105
8080chain 'J' and (resid 105 through 122 )JJ105 - 122106 - 123
8181chain 'J' and (resid 123 through 162 )JJ123 - 162124 - 161
8282chain 'J' and (resid 163 through 190 )JJ163 - 190162 - 189
8383chain 'J' and (resid 191 through 232 )JJ191 - 232190 - 231
8484chain 'K' and (resid 0 through 15 )KK0 - 151 - 16
8585chain 'K' and (resid 16 through 92 )KK16 - 9217 - 89
8686chain 'K' and (resid 93 through 122 )KK93 - 12290 - 119
8787chain 'K' and (resid 123 through 162 )KK123 - 162120 - 159
8888chain 'K' and (resid 163 through 180 )KK163 - 180160 - 177
8989chain 'K' and (resid 181 through 206 )KK181 - 206178 - 197
9090chain 'K' and (resid 207 through 232 )KK207 - 232198 - 223
9191chain 'L' and (resid 0 through 15 )LL0 - 151 - 16
9292chain 'L' and (resid 16 through 30 )LL16 - 3017 - 31
9393chain 'L' and (resid 31 through 64 )LL31 - 6432 - 65
9494chain 'L' and (resid 65 through 92 )LL65 - 9266 - 93
9595chain 'L' and (resid 93 through 127 )LL93 - 12794 - 128
9696chain 'L' and (resid 128 through 152 )LL128 - 152129 - 151
9797chain 'L' and (resid 153 through 171 )LL153 - 171152 - 170
9898chain 'L' and (resid 172 through 188 )LL172 - 188171 - 187
9999chain 'L' and (resid 189 through 219 )LL189 - 219188 - 210
100100chain 'L' and (resid 220 through 234 )LL220 - 234211 - 225
101101chain 'M' and (resid 0 through 15 )MM0 - 151 - 16
102102chain 'M' and (resid 16 through 30 )MM16 - 3017 - 31
103103chain 'M' and (resid 31 through 53 )MM31 - 5332 - 54
104104chain 'M' and (resid 54 through 92 )MM54 - 9255 - 93
105105chain 'M' and (resid 93 through 122 )MM93 - 12294 - 123
106106chain 'M' and (resid 123 through 143 )MM123 - 143124 - 144
107107chain 'M' and (resid 144 through 162 )MM144 - 162145 - 163
108108chain 'M' and (resid 163 through 180 )MM163 - 180164 - 181
109109chain 'M' and (resid 181 through 209 )MM181 - 209182 - 203
110110chain 'M' and (resid 210 through 232 )MM210 - 232204 - 226
111111chain 'N' and (resid 0 through 15 )NN0 - 151 - 16
112112chain 'N' and (resid 16 through 30 )NN16 - 3017 - 31
113113chain 'N' and (resid 31 through 64 )NN31 - 6432 - 65
114114chain 'N' and (resid 65 through 92 )NN65 - 9266 - 93
115115chain 'N' and (resid 93 through 133 )NN93 - 13394 - 134
116116chain 'N' and (resid 139 through 162 )NN139 - 162135 - 158
117117chain 'N' and (resid 163 through 209 )NN163 - 209159 - 201
118118chain 'N' and (resid 210 through 232 )NN210 - 232202 - 224
119119chain 'O' and (resid 0 through 15 )OO0 - 151 - 16
120120chain 'O' and (resid 16 through 30 )OO16 - 3017 - 31
121121chain 'O' and (resid 31 through 53 )OO31 - 5332 - 54
122122chain 'O' and (resid 54 through 104 )OO54 - 10455 - 105
123123chain 'O' and (resid 105 through 116 )OO105 - 116106 - 117
124124chain 'O' and (resid 117 through 127 )OO117 - 127118 - 128
125125chain 'O' and (resid 128 through 138 )OO128 - 138129 - 139
126126chain 'O' and (resid 139 through 162 )OO139 - 162140 - 163
127127chain 'O' and (resid 163 through 180 )OO163 - 180164 - 181
128128chain 'O' and (resid 181 through 209 )OO181 - 209182 - 202
129129chain 'O' and (resid 210 through 234 )OO210 - 234203 - 227
130130chain 'P' and (resid 0 through 15 )PP0 - 151 - 16
131131chain 'P' and (resid 16 through 30 )PP16 - 3017 - 31
132132chain 'P' and (resid 31 through 53 )PP31 - 5332 - 54
133133chain 'P' and (resid 54 through 104 )PP54 - 10455 - 105
134134chain 'P' and (resid 105 through 143 )PP105 - 143106 - 144
135135chain 'P' and (resid 144 through 162 )PP144 - 162145 - 163
136136chain 'P' and (resid 163 through 206 )PP163 - 206164 - 201
137137chain 'P' and (resid 207 through 233 )PP207 - 233202 - 228

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万見について

-
お知らせ

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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

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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

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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

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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

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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。

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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