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- PDB-6pam: Structure of a bacterial Atm1-family ABC transporter with MgADP bound -

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基本情報

登録情報
データベース: PDB / ID: 6pam
タイトルStructure of a bacterial Atm1-family ABC transporter with MgADP bound
要素ATM1-type heavy metal exporter
キーワードTRANSPORT PROTEIN / ABC transporter / ABC exporter / ATPase / membrane protein
機能・相同性
機能・相同性情報


トランスロカーゼ / response to mercury ion / ABC-type transporter activity / monoatomic ion transport / ATP hydrolysis activity / ATP binding / plasma membrane
類似検索 - 分子機能
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / ATM1-type heavy metal exporter
類似検索 - 構成要素
生物種Novosphingobium aromaticivorans (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.7 Å
データ登録者Fan, C. / Kaiser, J.T. / Rees, D.C.
資金援助 米国, 1件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
引用ジャーナル: Proc Natl Acad Sci U S A / 年: 2020
タイトル: A structural framework for unidirectional transport by a bacterial ABC exporter.
著者: Chengcheng Fan / Jens T Kaiser / Douglas C Rees /
要旨: The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from (Atm1) can export glutathione derivatives and confer ...The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from (Atm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the Atm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As Atm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by Atm1. One of the disulfide crosslinked Atm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.
履歴
登録2019年6月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年6月24日Provider: repository / タイプ: Initial release
改定 1.12020年8月19日Group: Database references / Derived calculations / カテゴリ: citation / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_label_asym_id
改定 1.22020年8月26日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: ATM1-type heavy metal exporter
B: ATM1-type heavy metal exporter
C: ATM1-type heavy metal exporter
D: ATM1-type heavy metal exporter
E: ATM1-type heavy metal exporter
F: ATM1-type heavy metal exporter
G: ATM1-type heavy metal exporter
H: ATM1-type heavy metal exporter
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)546,04124
ポリマ－542,4298
非ポリマー3,61216
水00
1
A: ATM1-type heavy metal exporter
B: ATM1-type heavy metal exporter
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,5106
ポリマ－135,6072
非ポリマー9034
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint-110 kcal/mol
Surface area53320 Å2
手法PISA
2
C: ATM1-type heavy metal exporter
D: ATM1-type heavy metal exporter
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,5106
ポリマ－135,6072
非ポリマー9034
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-112 kcal/mol
Surface area52810 Å2
手法PISA
3
E: ATM1-type heavy metal exporter
F: ATM1-type heavy metal exporter
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,5106
ポリマ－135,6072
非ポリマー9034
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14670 Å2
ΔGint-109 kcal/mol
Surface area54230 Å2
手法PISA
4
G: ATM1-type heavy metal exporter
H: ATM1-type heavy metal exporter
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,5106
ポリマ－135,6072
非ポリマー9034
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-115 kcal/mol
Surface area53540 Å2
手法PISA
単位格子
Length a, b, c (Å)129.180, 133.610, 134.260
Angle α, β, γ (deg.)110.620, 98.280, 101.200
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 16 or resid 19 through 20...
21(chain B and (resid 16 or resid 19 through 20...
31(chain C and (resid 16 or resid 19 through 20...
41(chain D and (resid 16 or resid 19 through 20...
51(chain E and (resid 16 or resid 19 through 20...
61(chain F and (resid 16 or resid 19 through 20...
12(chain G and (resid 14 through 73 or resid 75...
22(chain H and (resid 14 through 73 or resid 75...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 16 or resid 19 through 20...A16
121(chain A and (resid 16 or resid 19 through 20...A19 - 20
131(chain A and (resid 16 or resid 19 through 20...A22 - 27
141(chain A and (resid 16 or resid 19 through 20...A38 - 72
151(chain A and (resid 16 or resid 19 through 20...A75
161(chain A and (resid 16 or resid 19 through 20...A8 - 126
171(chain A and (resid 16 or resid 19 through 20...A134
181(chain A and (resid 16 or resid 19 through 20...A140
191(chain A and (resid 16 or resid 19 through 20...A142
1101(chain A and (resid 16 or resid 19 through 20...A42
1111(chain A and (resid 16 or resid 19 through 20...A1 - 148
1121(chain A and (resid 16 or resid 19 through 20...A150 - 159
1131(chain A and (resid 16 or resid 19 through 20...A0
1141(chain A and (resid 16 or resid 19 through 20...A185
1151(chain A and (resid 16 or resid 19 through 20...A13 - 702
1161(chain A and (resid 16 or resid 19 through 20...A335 - 341
1171(chain A and (resid 16 or resid 19 through 20...A13 - 702
1181(chain A and (resid 16 or resid 19 through 20...A349 - 357
1191(chain A and (resid 16 or resid 19 through 20...A13 - 702
1201(chain A and (resid 16 or resid 19 through 20...A384 - 420
1211(chain A and (resid 16 or resid 19 through 20...A13 - 702
1221(chain A and (resid 16 or resid 19 through 20...A422 - 463
1231(chain A and (resid 16 or resid 19 through 20...A0
1241(chain A and (resid 16 or resid 19 through 20...A491 - 493
1251(chain A and (resid 16 or resid 19 through 20...A532 - 580
1261(chain A and (resid 16 or resid 19 through 20...A532 - 584
1271(chain A and (resid 16 or resid 19 through 20...A586 - 598
211(chain B and (resid 16 or resid 19 through 20...B16
221(chain B and (resid 16 or resid 19 through 20...B19 - 20
231(chain B and (resid 16 or resid 19 through 20...B22 - 27
241(chain B and (resid 16 or resid 19 through 20...B29
251(chain B and (resid 16 or resid 19 through 20...B33 - 34
261(chain B and (resid 16 or resid 19 through 20...B38 - 72
271(chain B and (resid 16 or resid 19 through 20...B75 - 106
281(chain B and (resid 16 or resid 19 through 20...B108 - 126
291(chain B and (resid 16 or resid 19 through 20...B134
2101(chain B and (resid 16 or resid 19 through 20...B138
2111(chain B and (resid 16 or resid 19 through 20...B140
2121(chain B and (resid 16 or resid 19 through 20...B142
2131(chain B and (resid 16 or resid 19 through 20...B147 - 1159
2141(chain B and (resid 16 or resid 19 through 20...B161 - 179
2151(chain B and (resid 16 or resid 19 through 20...B18 - 179
2161(chain B and (resid 16 or resid 19 through 20...B181 - 245
2171(chain B and (resid 16 or resid 19 through 20...B247 - 259
2181(chain B and (resid 16 or resid 19 through 20...B261 - 333
2191(chain B and (resid 16 or resid 19 through 20...B335 - 341
2201(chain B and (resid 16 or resid 19 through 20...B344
2211(chain B and (resid 16 or resid 19 through 20...B384 - 420
2221(chain B and (resid 16 or resid 19 through 20...B422 - 463
2231(chain B and (resid 16 or resid 19 through 20...B465 - 471
2241(chain B and (resid 16 or resid 19 through 20...B473 - 489
2251(chain B and (resid 16 or resid 19 through 20...B491 - 493
2261(chain B and (resid 16 or resid 19 through 20...B495 - 530
2271(chain B and (resid 16 or resid 19 through 20...B532 - 584
2281(chain B and (resid 16 or resid 19 through 20...B586 - 598
311(chain C and (resid 16 or resid 19 through 20...C16
321(chain C and (resid 16 or resid 19 through 20...C19 - 20
331(chain C and (resid 16 or resid 19 through 20...C22 - 27
341(chain C and (resid 16 or resid 19 through 20...C29
351(chain C and (resid 16 or resid 19 through 20...C33 - 34
361(chain C and (resid 16 or resid 19 through 20...C38 - 72
371(chain C and (resid 16 or resid 19 through 20...C75 - 106
381(chain C and (resid 16 or resid 19 through 20...C108 - 126
391(chain C and (resid 16 or resid 19 through 20...C134
3101(chain C and (resid 16 or resid 19 through 20...C138
3111(chain C and (resid 16 or resid 19 through 20...C140
3121(chain C and (resid 16 or resid 19 through 20...C142
3131(chain C and (resid 16 or resid 19 through 20...C147 - 1159
3141(chain C and (resid 16 or resid 19 through 20...C161 - 179
3151(chain C and (resid 16 or resid 19 through 20...C18 - 179
3161(chain C and (resid 16 or resid 19 through 20...C181 - 245
3171(chain C and (resid 16 or resid 19 through 20...C247 - 259
3181(chain C and (resid 16 or resid 19 through 20...C261 - 333
3191(chain C and (resid 16 or resid 19 through 20...C335 - 341
3201(chain C and (resid 16 or resid 19 through 20...C344
3211(chain C and (resid 16 or resid 19 through 20...C384 - 420
3221(chain C and (resid 16 or resid 19 through 20...C422 - 463
3231(chain C and (resid 16 or resid 19 through 20...C465 - 471
3241(chain C and (resid 16 or resid 19 through 20...C473 - 489
3251(chain C and (resid 16 or resid 19 through 20...C491 - 493
3261(chain C and (resid 16 or resid 19 through 20...C495 - 530
3271(chain C and (resid 16 or resid 19 through 20...C532 - 584
3281(chain C and (resid 16 or resid 19 through 20...C586 - 598
411(chain D and (resid 16 or resid 19 through 20...D16
421(chain D and (resid 16 or resid 19 through 20...D19 - 20
431(chain D and (resid 16 or resid 19 through 20...D22 - 27
441(chain D and (resid 16 or resid 19 through 20...D29
451(chain D and (resid 16 or resid 19 through 20...D33 - 34
461(chain D and (resid 16 or resid 19 through 20...D38 - 72
471(chain D and (resid 16 or resid 19 through 20...D75 - 106
481(chain D and (resid 16 or resid 19 through 20...D108 - 126
491(chain D and (resid 16 or resid 19 through 20...D134
4101(chain D and (resid 16 or resid 19 through 20...D138
4111(chain D and (resid 16 or resid 19 through 20...D140
4121(chain D and (resid 16 or resid 19 through 20...D142
4131(chain D and (resid 16 or resid 19 through 20...D147 - 1159
4141(chain D and (resid 16 or resid 19 through 20...D161 - 179
4151(chain D and (resid 16 or resid 19 through 20...D18 - 179
4161(chain D and (resid 16 or resid 19 through 20...D181 - 245
4171(chain D and (resid 16 or resid 19 through 20...D247 - 259
4181(chain D and (resid 16 or resid 19 through 20...D261 - 333
4191(chain D and (resid 16 or resid 19 through 20...D335 - 341
4201(chain D and (resid 16 or resid 19 through 20...D344
4211(chain D and (resid 16 or resid 19 through 20...D384 - 420
4221(chain D and (resid 16 or resid 19 through 20...D422 - 463
4231(chain D and (resid 16 or resid 19 through 20...D465 - 471
4241(chain D and (resid 16 or resid 19 through 20...D473 - 489
4251(chain D and (resid 16 or resid 19 through 20...D491 - 493
4261(chain D and (resid 16 or resid 19 through 20...D495 - 530
4271(chain D and (resid 16 or resid 19 through 20...D532 - 584
4281(chain D and (resid 16 or resid 19 through 20...D586 - 598
511(chain E and (resid 16 or resid 19 through 20...E16
521(chain E and (resid 16 or resid 19 through 20...E19 - 20
531(chain E and (resid 16 or resid 19 through 20...E22 - 27
541(chain E and (resid 16 or resid 19 through 20...E29
551(chain E and (resid 16 or resid 19 through 20...E33 - 34
561(chain E and (resid 16 or resid 19 through 20...E38 - 72
571(chain E and (resid 16 or resid 19 through 20...E75 - 106
581(chain E and (resid 16 or resid 19 through 20...E108 - 126
591(chain E and (resid 16 or resid 19 through 20...E134
5101(chain E and (resid 16 or resid 19 through 20...E138
5111(chain E and (resid 16 or resid 19 through 20...E140
5121(chain E and (resid 16 or resid 19 through 20...E142
5131(chain E and (resid 16 or resid 19 through 20...E147 - 1159
5141(chain E and (resid 16 or resid 19 through 20...E161 - 179
5151(chain E and (resid 16 or resid 19 through 20...E18 - 179
5161(chain E and (resid 16 or resid 19 through 20...E181 - 245
5171(chain E and (resid 16 or resid 19 through 20...E247 - 259
5181(chain E and (resid 16 or resid 19 through 20...E261 - 333
5191(chain E and (resid 16 or resid 19 through 20...E335 - 341
5201(chain E and (resid 16 or resid 19 through 20...E344
5211(chain E and (resid 16 or resid 19 through 20...E384 - 420
5221(chain E and (resid 16 or resid 19 through 20...E422 - 463
5231(chain E and (resid 16 or resid 19 through 20...E465 - 471
5241(chain E and (resid 16 or resid 19 through 20...E473 - 489
5251(chain E and (resid 16 or resid 19 through 20...E491 - 493
5261(chain E and (resid 16 or resid 19 through 20...E495 - 530
5271(chain E and (resid 16 or resid 19 through 20...E532 - 584
5281(chain E and (resid 16 or resid 19 through 20...E586 - 598
611(chain F and (resid 16 or resid 19 through 20...F16
621(chain F and (resid 16 or resid 19 through 20...F19 - 20
631(chain F and (resid 16 or resid 19 through 20...F22 - 27
641(chain F and (resid 16 or resid 19 through 20...F29
651(chain F and (resid 16 or resid 19 through 20...F33 - 34
661(chain F and (resid 16 or resid 19 through 20...F38 - 72
671(chain F and (resid 16 or resid 19 through 20...F75 - 106
681(chain F and (resid 16 or resid 19 through 20...F108 - 126
691(chain F and (resid 16 or resid 19 through 20...F134
6101(chain F and (resid 16 or resid 19 through 20...F138
6111(chain F and (resid 16 or resid 19 through 20...F140
6121(chain F and (resid 16 or resid 19 through 20...F142
6131(chain F and (resid 16 or resid 19 through 20...F147 - 1159
6141(chain F and (resid 16 or resid 19 through 20...F161 - 179
6151(chain F and (resid 16 or resid 19 through 20...F18 - 179
6161(chain F and (resid 16 or resid 19 through 20...F181 - 245
6171(chain F and (resid 16 or resid 19 through 20...F247 - 259
6181(chain F and (resid 16 or resid 19 through 20...F261 - 333
6191(chain F and (resid 16 or resid 19 through 20...F335 - 341
6201(chain F and (resid 16 or resid 19 through 20...F344
6211(chain F and (resid 16 or resid 19 through 20...F384 - 420
6221(chain F and (resid 16 or resid 19 through 20...F422 - 463
6231(chain F and (resid 16 or resid 19 through 20...F465 - 471
6241(chain F and (resid 16 or resid 19 through 20...F473 - 489
6251(chain F and (resid 16 or resid 19 through 20...F491 - 493
6261(chain F and (resid 16 or resid 19 through 20...F495 - 530
6271(chain F and (resid 16 or resid 19 through 20...F532 - 584
6281(chain F and (resid 16 or resid 19 through 20...F586 - 598
112(chain G and (resid 14 through 73 or resid 75...G14 - 73
122(chain G and (resid 14 through 73 or resid 75...G75 - 124
132(chain G and (resid 14 through 73 or resid 75...G127 - 129
142(chain G and (resid 14 through 73 or resid 75...G138
152(chain G and (resid 14 through 73 or resid 75...G13 - 702
162(chain G and (resid 14 through 73 or resid 75...G13 - 702
172(chain G and (resid 14 through 73 or resid 75...G150 - 231
182(chain G and (resid 14 through 73 or resid 75...G354
192(chain G and (resid 14 through 73 or resid 75...G354
1102(chain G and (resid 14 through 73 or resid 75...G0
1112(chain G and (resid 14 through 73 or resid 75...G483 - 554
1122(chain G and (resid 14 through 73 or resid 75...G556 - 601
212(chain H and (resid 14 through 73 or resid 75...H14 - 73
222(chain H and (resid 14 through 73 or resid 75...H75 - 124
232(chain H and (resid 14 through 73 or resid 75...H127 - 129
242(chain H and (resid 14 through 73 or resid 75...H138
252(chain H and (resid 14 through 73 or resid 75...H13 - 702
262(chain H and (resid 14 through 73 or resid 75...H13 - 702
272(chain H and (resid 14 through 73 or resid 75...H150 - 231
282(chain H and (resid 14 through 73 or resid 75...H354
292(chain H and (resid 14 through 73 or resid 75...H354
2102(chain H and (resid 14 through 73 or resid 75...H0
2112(chain H and (resid 14 through 73 or resid 75...H483 - 554
2122(chain H and (resid 14 through 73 or resid 75...H556 - 601

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
ATM1-type heavy metal exporter / ATP-binding cassette transporter Atm1 / NaAtm1


分子量: 67803.664 Da / 分子数: 8 / 変異: A527C / 由来タイプ: 組換発現
由来: (組換発現) Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199) (バクテリア)
株: ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199
遺伝子: atm1, Saro_2631 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q2G506
#2: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


分子量: 427.201 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM
#3: 化合物
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Mg
研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 3.82 Å3/Da / 溶媒含有率: 67.77 % / 解説: Thin plates
結晶化温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.3 / 詳細: NaCl, MgCl2, Tris, PEG2000MME, ATP

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データ収集

回折
ID平均測定温度 (K)Crystal-IDSerial crystal experiment
11001N
21001N
放射光源
由来サイトビームラインID波長 (Å)
シンクロトロンSSRL BL12-210.97946
シンクロトロンSSRL BL12-220.97949
検出器
タイプID検出器日付
DECTRIS PILATUS 6M1PIXEL2016年6月25日
DECTRIS PILATUS 6M2PIXEL2016年11月18日
放射
IDモノクロメータープロトコル単色(M)・ラウエ(L)散乱光タイプWavelength-ID
1Liquid nitrogen-cooled double crystal, non fixed exit slit Si(111)SINGLE WAVELENGTHMx-ray1
2Liquid nitrogen-cooled double crystal, non fixed exit slit Si(111)SINGLE WAVELENGTHMx-ray2
放射波長
ID波長 (Å)相対比
10.979461
20.979491
反射

Entry-ID: 6PAM

解像度 (Å)Num. obs% possible obs (%)冗長度 (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
3.7-39.618462897.557.1141.790.9990.1670.0670.1817.31
4.5-39.724727799.320.6163.640.9980.2910.0660.29828.1
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
3.7-3.8327.33.050.7476460.4121.2063.283189.28
4.5-4.6621.43.2411.446670.7610.7123.32299.3

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
REFMAC精密化
PHASER位相決定
AutoSol位相決定
PDB_EXTRACTデータ抽出
Aimlessデータスケーリング
XDSデータ削減
Blu-Iceデータ収集
精密化構造決定の手法: 分子置換
開始モデル: 4MRN

4mrn


解像度: 3.7→39.606 Å / SU ML: 0.57 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 34.98
Rfactor反射数%反射
Rfree0.2858 4185 5.01 %
Rwork0.2382 --
obs0.2406 83474 97.63 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 456.95 Å2 / Biso mean: 178.1364 Å2 / Biso min: 31.35 Å2
精密化ステップサイクル: final / 解像度: 3.7→39.606 Å
タンパク質核酸リガンド溶媒全体
原子数36615 0 224 0 36839
Biso mean--194.08 --
残基数----4706
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A14398X-RAY DIFFRACTION8.88TORSIONAL
12B14398X-RAY DIFFRACTION8.88TORSIONAL
13C14398X-RAY DIFFRACTION8.88TORSIONAL
14D14398X-RAY DIFFRACTION8.88TORSIONAL
15E14398X-RAY DIFFRACTION8.88TORSIONAL
16F14398X-RAY DIFFRACTION8.88TORSIONAL
21G5244X-RAY DIFFRACTION8.88TORSIONAL
22H5244X-RAY DIFFRACTION8.88TORSIONAL
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 (%)
3.7-3.7420.38121180.37612240235883
3.742-3.7860.44991170.35232465258291
3.786-3.83220.35681110.33672592270394
3.8322-3.88060.41121570.33632508266596
3.8806-3.93160.39541590.34812657281697
3.9316-3.98550.38791380.33612630276897
3.9855-4.04230.36911620.30652625278798
4.0423-4.10260.34531380.27822674281299
4.1026-4.16670.32081420.27362690283299
4.1667-4.23490.3711310.26512678280999
4.2349-4.30780.31341380.26282718285699
4.3078-4.38610.33771840.25442564274899
4.3861-4.47030.2991440.24312699284399
4.4703-4.56140.31011610.23352606276798
4.5614-4.66050.3021300.20662705283599
4.6605-4.76870.22771110.19172768287999
4.7687-4.88780.32041410.19042640278199
4.8878-5.01970.25681650.18552592275798
5.0197-5.16710.23351550.20012713286899
5.1671-5.33350.28161400.21182631277198
5.3335-5.52360.27151410.23152689283099
5.5236-5.74410.2981330.23882695282899
5.7441-6.00470.27511200.23032720284099
6.0047-6.32010.32671290.23252691282099
6.3201-6.71430.29071360.22482707284399
6.7143-7.22980.30881590.22912668282799
7.2298-7.95210.2861230.207827182841100
7.9521-9.09060.20731370.17962683282099
9.0906-11.40760.20261350.18222670280599
11.4076-39.60850.28691300.29512653278397

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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