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- PDB-6aoc: Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase... -

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基本情報

登録情報
データベース: PDB / ID: 6aoc
タイトルCrystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase
要素
  • Reverse transcriptase/ribonuclease H
  • p51 RT
キーワードTRANSFERASE / TRANSFERASE INHIBITOR / HIV-1 / TRANSFERASE - TRANSFERASE INHIBITOR complex
機能・相同性
機能・相同性情報


RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / 加水分解酵素; エステル加水分解酵素 / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
類似検索 - 分子機能
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
: / TRIETHYLENE GLYCOL / Chem-ZW2 / Gag-Pol polyprotein
類似検索 - 構成要素
生物種Human immunodeficiency virus type 1 group M subtype B (ヒト免疫不全ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.8 Å
データ登録者Kirby, K.A. / Sarafianos, S.G.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100890 米国
引用ジャーナル: Eur J Med Chem / 年: 2017
タイトル: Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H.
著者: Kankanala, J. / Kirby, K.A. / Huber, A.D. / Casey, M.C. / Wilson, D.J. / Sarafianos, S.G. / Wang, Z.
履歴
登録2017年8月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年8月8日Provider: repository / タイプ: Initial release
改定 1.12019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22023年10月4日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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

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集合体

登録構造単位
A: Reverse transcriptase/ribonuclease H
B: p51 RT
C: Reverse transcriptase/ribonuclease H
D: p51 RT
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)234,44485
ポリマ－228,4044
非ポリマー6,04081
水20,6631147
1
A: Reverse transcriptase/ribonuclease H
B: p51 RT
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)117,38543
ポリマ－114,2022
非ポリマー3,18341
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint46 kcal/mol
Surface area47030 Å2
手法PISA
2
C: Reverse transcriptase/ribonuclease H
D: p51 RT
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)117,05942
ポリマ－114,2022
非ポリマー2,85740
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint84 kcal/mol
Surface area47420 Å2
手法PISA
単位格子
Length a, b, c (Å)70.370, 89.120, 112.730
Angle α, β, γ (deg.)105.720, 95.030, 110.720
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 1 through 21 or resid 23...
21(chain C and (resid 1 through 21 or resid 23...
12(chain B and (resid 4 through 21 or resid 23...
22(chain D and (resid 4 through 21 or resid 23...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 21 or resid 23...A1 - 21
121(chain A and (resid 1 through 21 or resid 23...A23 - 39
131(chain A and (resid 1 through 21 or resid 23...A41 - 42
141(chain A and (resid 1 through 21 or resid 23...A44 - 52
151(chain A and (resid 1 through 21 or resid 23...A54 - 59
161(chain A and (resid 1 through 21 or resid 23...A61 - 71
171(chain A and (resid 1 through 21 or resid 23...A73 - 81
181(chain A and (resid 1 through 21 or resid 23...A83 - 103
191(chain A and (resid 1 through 21 or resid 23...A105 - 133
1101(chain A and (resid 1 through 21 or resid 23...A136 - 160
1111(chain A and (resid 1 through 21 or resid 23...A162 - 163
1121(chain A and (resid 1 through 21 or resid 23...A165 - 168
1131(chain A and (resid 1 through 21 or resid 23...A170 - 1781
1141(chain A and (resid 1 through 21 or resid 23...A183 - 198
1151(chain A and (resid 1 through 21 or resid 23...A200198
1161(chain A and (resid 1 through 21 or resid 23...A200 - 211
1171(chain A and (resid 1 through 21 or resid 23...A213 - 296
1181(chain A and (resid 1 through 21 or resid 23...A304
1191(chain A and (resid 1 through 21 or resid 23...A312
1201(chain A and (resid 1 through 21 or resid 23...A308 - 321
1211(chain A and (resid 1 through 21 or resid 23...A363
1221(chain A and (resid 1 through 21 or resid 23...A363
1231(chain A and (resid 1 through 21 or resid 23...A365 - 366
1241(chain A and (resid 1 through 21 or resid 23...A374 - 385
1251(chain A and (resid 1 through 21 or resid 23...A393 - 394
1261(chain A and (resid 1 through 21 or resid 23...A403 - 398
1271(chain A and (resid 1 through 21 or resid 23...A406 - 4006
1281(chain A and (resid 1 through 21 or resid 23...A414 - 416
1291(chain A and (resid 1 through 21 or resid 23...A424416
1301(chain A and (resid 1 through 21 or resid 23...A424 - 427
1311(chain A and (resid 1 through 21 or resid 23...A429 - 447
1321(chain A and (resid 1 through 21 or resid 23...A450 - 460
1331(chain A and (resid 1 through 21 or resid 23...A462 - 466
1341(chain A and (resid 1 through 21 or resid 23...A468 - 4706
1351(chain A and (resid 1 through 21 or resid 23...A508
1361(chain A and (resid 1 through 21 or resid 23...A510 - 511
1371(chain A and (resid 1 through 21 or resid 23...A513 - 519
1381(chain A and (resid 1 through 21 or resid 23...A521 - 522
1391(chain A and (resid 1 through 21 or resid 23...A524 - 539
1401(chain A and (resid 1 through 21 or resid 23...A541 - 542
1411(chain A and (resid 1 through 21 or resid 23...A545 - 546
1421(chain A and (resid 1 through 21 or resid 23...A548 - 555
211(chain C and (resid 1 through 21 or resid 23...C1 - 21
221(chain C and (resid 1 through 21 or resid 23...C23 - 39
231(chain C and (resid 1 through 21 or resid 23...C41 - 42
241(chain C and (resid 1 through 21 or resid 23...C-1 - 59
251(chain C and (resid 1 through 21 or resid 23...C61 - 71
261(chain C and (resid 1 through 21 or resid 23...C73 - 81
271(chain C and (resid 1 through 21 or resid 23...C-1 - 562
281(chain C and (resid 1 through 21 or resid 23...C105 - 133
291(chain C and (resid 1 through 21 or resid 23...C162 - 163
2101(chain C and (resid 1 through 21 or resid 23...C173 - 181
2111(chain C and (resid 1 through 21 or resid 23...C173 - 181
2121(chain C and (resid 1 through 21 or resid 23...C183 - 198
2131(chain C and (resid 1 through 21 or resid 23...C200 - 211
2141(chain C and (resid 1 through 21 or resid 23...C304 - 306
2151(chain C and (resid 1 through 21 or resid 23...C312
2161(chain C and (resid 1 through 21 or resid 23...C329 - 352
2171(chain C and (resid 1 through 21 or resid 23...C360 - 355
2181(chain C and (resid 1 through 21 or resid 23...C360 - 355
2191(chain C and (resid 1 through 21 or resid 23...C363
2201(chain C and (resid 1 through 21 or resid 23...C374 - 385
2211(chain C and (resid 1 through 21 or resid 23...C393 - 394
2221(chain C and (resid 1 through 21 or resid 23...C403 - 398
2231(chain C and (resid 1 through 21 or resid 23...C403 - 398
2241(chain C and (resid 1 through 21 or resid 23...C414 - 416
2251(chain C and (resid 1 through 21 or resid 23...C424 - 426
2261(chain C and (resid 1 through 21 or resid 23...C450 - 467
2271(chain C and (resid 1 through 21 or resid 23...C429 - 447
2281(chain C and (resid 1 through 21 or resid 23...C462 - 460
2291(chain C and (resid 1 through 21 or resid 23...C468 - 476
2301(chain C and (resid 1 through 21 or resid 23...C477 - 505
2311(chain C and (resid 1 through 21 or resid 23...C508
2321(chain C and (resid 1 through 21 or resid 23...C513 - 519
2331(chain C and (resid 1 through 21 or resid 23...C521 - 522
2341(chain C and (resid 1 through 21 or resid 23...C521 - 522
2351(chain C and (resid 1 through 21 or resid 23...C545 - 542
2361(chain C and (resid 1 through 21 or resid 23...C545 - 546
2371(chain C and (resid 1 through 21 or resid 23...C548 - 555
112(chain B and (resid 4 through 21 or resid 23...B4 - 21
122(chain B and (resid 4 through 21 or resid 23...B23 - 27
132(chain B and (resid 4 through 21 or resid 23...B29
142(chain B and (resid 4 through 21 or resid 23...B31
152(chain B and (resid 4 through 21 or resid 23...B33 - 42
162(chain B and (resid 4 through 21 or resid 23...B0
172(chain B and (resid 4 through 21 or resid 23...B66
182(chain B and (resid 4 through 21 or resid 23...B0 - 72
192(chain B and (resid 4 through 21 or resid 23...B74 - 92
1102(chain B and (resid 4 through 21 or resid 23...B95 - 101
1112(chain B and (resid 4 through 21 or resid 23...B0 - 428
1122(chain B and (resid 4 through 21 or resid 23...B3 - 12225
1132(chain B and (resid 4 through 21 or resid 23...B0 - 428
1142(chain B and (resid 4 through 21 or resid 23...B127 - 139
1152(chain B and (resid 4 through 21 or resid 23...B0
1162(chain B and (resid 4 through 21 or resid 23...B170 - 171
1172(chain B and (resid 4 through 21 or resid 23...B173
1182(chain B and (resid 4 through 21 or resid 23...B175 - 183
1192(chain B and (resid 4 through 21 or resid 23...B185 - 196
1202(chain B and (resid 4 through 21 or resid 23...B207 - 214
1212(chain B and (resid 4 through 21 or resid 23...B226 - 22
1222(chain B and (resid 4 through 21 or resid 23...B235
1232(chain B and (resid 4 through 21 or resid 23...B243
1242(chain B and (resid 4 through 21 or resid 23...B245 - 240
1252(chain B and (resid 4 through 21 or resid 23...B248 - 245
1262(chain B and (resid 4 through 21 or resid 23...B287 - 282
1272(chain B and (resid 4 through 21 or resid 23...B290 - 30
1282(chain B and (resid 4 through 21 or resid 23...B315 - 310
1292(chain B and (resid 4 through 21 or resid 23...B318
1302(chain B and (resid 4 through 21 or resid 23...B326 - 321
1312(chain B and (resid 4 through 21 or resid 23...B329 - 331
1322(chain B and (resid 4 through 21 or resid 23...B339
1332(chain B and (resid 4 through 21 or resid 23...B347 - 351
1342(chain B and (resid 4 through 21 or resid 23...B359 - 374
1352(chain B and (resid 4 through 21 or resid 23...B382 - 383
1362(chain B and (resid 4 through 21 or resid 23...B391 - 389
1372(chain B and (resid 4 through 21 or resid 23...B397 - 402
1382(chain B and (resid 4 through 21 or resid 23...B410 - 408
1392(chain B and (resid 4 through 21 or resid 23...B416 - 414
1402(chain B and (resid 4 through 21 or resid 23...B422 - 424
212(chain D and (resid 4 through 21 or resid 23...D4 - 21
222(chain D and (resid 4 through 21 or resid 23...D23 - 27
232(chain D and (resid 4 through 21 or resid 23...D29
242(chain D and (resid 4 through 21 or resid 23...D3
252(chain D and (resid 4 through 21 or resid 23...D33 - 44
262(chain D and (resid 4 through 21 or resid 23...D44 - 54
272(chain D and (resid 4 through 21 or resid 23...D5
282(chain D and (resid 4 through 21 or resid 23...D4 - 428
292(chain D and (resid 4 through 21 or resid 23...D4 - 428
2102(chain D and (resid 4 through 21 or resid 23...D95 - 101
2112(chain D and (resid 4 through 21 or resid 23...D4 - 428
2122(chain D and (resid 4 through 21 or resid 23...D127 - 139
2132(chain D and (resid 4 through 21 or resid 23...D167 - 168
2142(chain D and (resid 4 through 21 or resid 23...D167 - 168
2152(chain D and (resid 4 through 21 or resid 23...D170 - 171
2162(chain D and (resid 4 through 21 or resid 23...D173
2172(chain D and (resid 4 through 21 or resid 23...D185 - 196
2182(chain D and (resid 4 through 21 or resid 23...D198 - 205
2192(chain D and (resid 4 through 21 or resid 23...D207 - 225
2202(chain D and (resid 4 through 21 or resid 23...D207 - 225
2212(chain D and (resid 4 through 21 or resid 23...D246 - 243
2222(chain D and (resid 4 through 21 or resid 23...D246 - 243
2232(chain D and (resid 4 through 21 or resid 23...D285 - 280
2242(chain D and (resid 4 through 21 or resid 23...D313 - 305
2252(chain D and (resid 4 through 21 or resid 23...D324 - 318
2262(chain D and (resid 4 through 21 or resid 23...D316
2272(chain D and (resid 4 through 21 or resid 23...D327 - 329
2282(chain D and (resid 4 through 21 or resid 23...D337 - 339
2292(chain D and (resid 4 through 21 or resid 23...D345 - 347
2302(chain D and (resid 4 through 21 or resid 23...D357 - 379
2312(chain D and (resid 4 through 21 or resid 23...D380 - 382
2322(chain D and (resid 4 through 21 or resid 23...D389 - 381
2332(chain D and (resid 4 through 21 or resid 23...D395 - 407
2342(chain D and (resid 4 through 21 or resid 23...D408 - 400
2352(chain D and (resid 4 through 21 or resid 23...D414 - 416
2362(chain D and (resid 4 through 21 or resid 23...D414 - 412
2372(chain D and (resid 4 through 21 or resid 23...D420 - 422

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 2種, 4分子 ACBD

#1: タンパク質 Reverse transcriptase/ribonuclease H


分子量: 64105.441 Da / 分子数: 2 / 断片: p66 domain residues 168-722 / 変異: C280S / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (ヒト免疫不全ウイルス)
株: isolate BH10 / 遺伝子: gag-pol / プラスミド: pET35a / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) RIL
参照: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: タンパク質 p51 RT / Exoribonuclease H / p66 RT


分子量: 50096.539 Da / 分子数: 2 / 断片: p51 domain residues 168-595 / 変異: C280S / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (ヒト免疫不全ウイルス)
株: isolate BH10 / 遺伝子: gag-pol / プラスミド: pET35a / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) RIL / 参照: UniProt: P03366

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非ポリマー , 5種, 1228分子

#3: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mn
#4: 化合物 ChemComp-ZW2 / 6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione


分子量: 274.295 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C13H10N2O3S
#5: 化合物
ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C6H14O4
#6: 化合物...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 68 / 由来タイプ: 合成 / 式: C2H6O2
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1147 / 由来タイプ: 天然 / 式: H2O

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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: 2.73 Å3/Da / 溶媒含有率: 54.92 % / Mosaicity: 0.139 °
結晶化温度: 291 K / 手法: 蒸気拡散法 / pH: 6
詳細: PEG 3350, SODIUM POTASSIUM PHOSPHATE, ETHYLENE GLYCOL, TRIS

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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: 23-ID-D / 波長: 1.033 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年7月30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: 1.033 Å / 相対比: 1
反射解像度: 1.8→55.32 Å / Num. obs: 217194 / % possible obs: 97.1 % / 冗長度: 3.5 % / Biso Wilson estimate: 36.81 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Net I/σ(I): 9.9 / Num. measured all: 761476
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.8-1.833.20.734281105750.9841.81294.6
4.88-55.343.529.938373110060.020.03898.3

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575)精密化
xia20.4.0.338データスケーリング
XDSデータ削減
PDB_EXTRACT3.22データ抽出
MrBUMP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4KFB

4kfb


解像度: 1.8→55.318 Å / SU ML: 0.27 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 26.87 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2258 10774 4.96 %
Rwork0.1863 206361 -
obs0.1883 217135 97.03 %
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 max: 196.69 Å2 / Biso mean: 61.5361 Å2 / Biso min: 22.92 Å2
精密化ステップサイクル: final / 解像度: 1.8→55.318 Å
タンパク質核酸リガンド溶媒全体
原子数15992 0 384 1147 17523
Biso mean--73.09 60.52 -
残基数----1950
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0117540
X-RAY DIFFRACTIONf_angle_d0.98323765
X-RAY DIFFRACTIONf_chiral_restr0.062533
X-RAY DIFFRACTIONf_plane_restr0.0082996
X-RAY DIFFRACTIONf_dihedral_angle_d18.94410781
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5967X-RAY DIFFRACTION9.484TORSIONAL
12C5967X-RAY DIFFRACTION9.484TORSIONAL
21B4441X-RAY DIFFRACTION9.484TORSIONAL
22D4441X-RAY DIFFRACTION9.484TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.38373380.37956607694593
1.8205-1.84190.37853750.35236812718796
1.8419-1.86430.37723520.32836751710396
1.8643-1.88790.37123650.31076789715496
1.8879-1.91280.34393420.29566808715096
1.9128-1.9390.28173730.27836836720996
1.939-1.96670.32513550.27226806716196
1.9667-1.99610.30663480.2716870721896
1.9961-2.02720.30683830.26026816719996
2.0272-2.06050.28153520.24876870722297
2.0605-2.0960.27343860.23466760714696
2.096-2.13410.25363240.22466911723597
2.1341-2.17520.25383400.21586889722997
2.1752-2.21960.24943370.20776854719197
2.2196-2.26780.25713250.20376948727397
2.2678-2.32060.23453510.19936875722697
2.3206-2.37860.223430.20126906724997
2.3786-2.44290.2493500.20286920727097
2.4429-2.51480.23913910.19296909730098
2.5148-2.5960.23573780.19156890726898
2.596-2.68880.23623730.19166929730298
2.6888-2.79640.21933310.19136978730998
2.7964-2.92370.22483450.19046976732198
2.9237-3.07780.24343590.19586953731298
3.0778-3.27060.243980.18466927732598
3.2706-3.52310.22393580.17687018737698
3.5231-3.87760.21913590.16076938729798
3.8776-4.43850.18143800.13986936731698
4.4385-5.59120.16483620.14276964732698
5.5912-55.34390.21924010.18686915731698
精密化 TLS手法: refined / Origin x: -12.6082 Å / Origin y: 29.8951 Å / Origin z: -11.1644 Å
111213212223313233
T0.2257 Å2-0.0231 Å20.0286 Å2-0.3088 Å2-0.0115 Å2--0.3325 Å2
L0.0302 °2-0.1207 °20.2069 °2-0.2402 °2-0.1516 °2--0.3924 °2
S-0.0046 Å °0.0361 Å °0.0006 Å °0.0018 Å °-0.005 Å °-0.0824 Å °-0.0477 Å °0.0284 Å °0.0195 Å °
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 562
2X-RAY DIFFRACTION1allB0 - 428
3X-RAY DIFFRACTION1allC-1 - 562
4X-RAY DIFFRACTION1allD4 - 428
5X-RAY DIFFRACTION1allL1 - 11
6X-RAY DIFFRACTION1allW1 - 1483
7X-RAY DIFFRACTION1allI1 - 90

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万見について

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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://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