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- PDB-6pfz: Structure of a NAD-Dependent Persulfide Reductase from A. fulgidus -

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基本情報

登録情報
データベース: PDB / ID: 6pfz
タイトルStructure of a NAD-Dependent Persulfide Reductase from A. fulgidus
要素NADH oxidase (NoxA-3)
キーワードFLAVOPROTEIN / NADH-dependent Reductase / persulfide reductase / disulfide reductase / polysulfide reductase
機能・相同性
機能・相同性情報


cell redox homeostasis / flavin adenine dinucleotide binding / oxidoreductase activity
類似検索 - 分子機能
Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase ...Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
類似検索 - ドメイン・相同性
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / NADH oxidase (NoxA-3)
類似検索 - 構成要素
生物種Archaeoglobus fulgidus DSM 4304 (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.10003870577 Å
データ登録者Sazinsky, M.H. / Shabdar, S. / Garcia-Constineiras, A. / Crane III, E.J.
資金援助 米国, 1件
組織認可番号国
National Science Foundation (NSF, United States)1518306 米国
引用ジャーナル: Archaea / 年: 2021
タイトル: Structural and Kinetic Characterization of Hyperthermophilic NADH-Dependent Persulfide Reductase from Archaeoglobus fulgidus .
著者: Shabdar, S. / Anaclet, B. / Castineiras, A.G. / Desir, N. / Choe, N. / Crane 3rd, E.J. / Sazinsky, M.H.
履歴
登録2019年6月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月1日Provider: repository / タイプ: Initial release
改定 1.12021年4月14日Group: Database references / Derived calculations / カテゴリ: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _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 / _struct_conn.ptnr2_label_seq_id
改定 1.22023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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
D: NADH oxidase (NoxA-3)
A: NADH oxidase (NoxA-3)
B: NADH oxidase (NoxA-3)
C: NADH oxidase (NoxA-3)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)247,38916
ポリマ－241,0164
非ポリマー6,37312
水25214
1
D: NADH oxidase (NoxA-3)
C: NADH oxidase (NoxA-3)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)123,6948
ポリマ－120,5082
非ポリマー3,1866
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-78 kcal/mol
Surface area38490 Å2
手法PISA
2
A: NADH oxidase (NoxA-3)
B: NADH oxidase (NoxA-3)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)123,6948
ポリマ－120,5082
非ポリマー3,1866
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-81 kcal/mol
Surface area38400 Å2
手法PISA
単位格子
Length a, b, c (Å)84.976, 100.355, 136.196
Angle α, β, γ (deg.)90.000, 91.894, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resseq 1:4 or (resid 5 and (name...AB1 - 331 - 33
12TYRTYRGLUGLU(chain A and (resseq 1:4 or (resid 5 and (name...AB36 - 6036 - 60
13ARGARGVALVAL(chain A and (resseq 1:4 or (resid 5 and (name...AB67 - 9967 - 99
14ASNASNILEILE(chain A and (resseq 1:4 or (resid 5 and (name...AB101 - 128101 - 128
15ALAALAGLUGLU(chain A and (resseq 1:4 or (resid 5 and (name...AB130 - 143130 - 143
16ILEILEGLYGLY(chain A and (resseq 1:4 or (resid 5 and (name...AB145 - 152145 - 152
17LYSLYSMETMET(chain A and (resseq 1:4 or (resid 5 and (name...AB155 - 177155 - 177
18VALVALASPASP(chain A and (resseq 1:4 or (resid 5 and (name...AB179 - 194179 - 194
19GLUGLUSERSER(chain A and (resseq 1:4 or (resid 5 and (name...AB196 - 223196 - 223
110ARGARGVALVAL(chain A and (resseq 1:4 or (resid 5 and (name...AB229 - 231229 - 231
111ASNASNILEILE(chain A and (resseq 1:4 or (resid 5 and (name...AB234 - 249234 - 249
112PROPROGLUGLU(chain A and (resseq 1:4 or (resid 5 and (name...AB251 - 257251 - 257
113ALAALAILEILE(chain A and (resseq 1:4 or (resid 5 and (name...AB259 - 263259 - 263
114THRTHRGLYGLY(chain A and (resseq 1:4 or (resid 5 and (name...AB266 - 321266 - 321
115ALAALATRPTRP(chain A and (resseq 1:4 or (resid 5 and (name...AB324 - 390324 - 390
116VALVALPHEPHE(chain A and (resseq 1:4 or (resid 5 and (name...AB392 - 462392 - 462
117ILEILESERSER(chain A and (resseq 1:4 or (resid 5 and (name...AB473 - 480473 - 480
118GLUGLUGLUGLU(chain A and (resseq 1:4 or (resid 5 and (name...AB483483
119LYSLYSARGARG(chain A and (resseq 1:4 or (resid 5 and (name...AB493 - 503493 - 503
120ARGARGLEULEU(chain A and (resseq 1:4 or (resid 5 and (name...AB505 - 506505 - 506
121GLUGLUPROPRO(chain A and (resseq 1:4 or (resid 5 and (name...AB508 - 510508 - 510
122LYSLYSLEULEU(chain A and (resseq 1:4 or (resid 5 and (name...AB513 - 532513 - 532
123ALAALAPHEPHE(chain A and (resseq 1:4 or (resid 5 and (name...AB535 - 537535 - 537
124LYSLYSPHEPHE(chain A and (resseq 1:4 or (resid 5 and (name...AB539 - 551539 - 551
125FADFADFADFAD(chain A and (resseq 1:4 or (resid 5 and (name...AG901
21METMETALAALA(chain B and (resseq 1:4 or (resid 5 and (name...BC1 - 331 - 33
22TYRTYRGLUGLU(chain B and (resseq 1:4 or (resid 5 and (name...BC36 - 6036 - 60
23ARGARGVALVAL(chain B and (resseq 1:4 or (resid 5 and (name...BC67 - 9967 - 99
24ASNASNILEILE(chain B and (resseq 1:4 or (resid 5 and (name...BC101 - 128101 - 128
25ALAALAGLUGLU(chain B and (resseq 1:4 or (resid 5 and (name...BC130 - 143130 - 143
26ILEILEGLYGLY(chain B and (resseq 1:4 or (resid 5 and (name...BC145 - 152145 - 152
27LYSLYSMETMET(chain B and (resseq 1:4 or (resid 5 and (name...BC155 - 177155 - 177
28VALVALASPASP(chain B and (resseq 1:4 or (resid 5 and (name...BC179 - 194179 - 194
29GLUGLUSERSER(chain B and (resseq 1:4 or (resid 5 and (name...BC196 - 223196 - 223
210ARGARGVALVAL(chain B and (resseq 1:4 or (resid 5 and (name...BC229 - 231229 - 231
211ASNASNILEILE(chain B and (resseq 1:4 or (resid 5 and (name...BC234 - 249234 - 249
212PROPROGLUGLU(chain B and (resseq 1:4 or (resid 5 and (name...BC251 - 257251 - 257
213ALAALAILEILE(chain B and (resseq 1:4 or (resid 5 and (name...BC259 - 263259 - 263
214THRTHRGLYGLY(chain B and (resseq 1:4 or (resid 5 and (name...BC266 - 321266 - 321
215ALAALATRPTRP(chain B and (resseq 1:4 or (resid 5 and (name...BC324 - 390324 - 390
216VALVALPHEPHE(chain B and (resseq 1:4 or (resid 5 and (name...BC392 - 462392 - 462
217ILEILESERSER(chain B and (resseq 1:4 or (resid 5 and (name...BC473 - 480473 - 480
218GLUGLUGLUGLU(chain B and (resseq 1:4 or (resid 5 and (name...BC483483
219LYSLYSARGARG(chain B and (resseq 1:4 or (resid 5 and (name...BC493 - 503493 - 503
220ARGARGLEULEU(chain B and (resseq 1:4 or (resid 5 and (name...BC505 - 506505 - 506
221GLUGLUPROPRO(chain B and (resseq 1:4 or (resid 5 and (name...BC508 - 510508 - 510
222LYSLYSLEULEU(chain B and (resseq 1:4 or (resid 5 and (name...BC513 - 532513 - 532
223ALAALAPHEPHE(chain B and (resseq 1:4 or (resid 5 and (name...BC535 - 537535 - 537
224LYSLYSPHEPHE(chain B and (resseq 1:4 or (resid 5 and (name...BC539 - 551539 - 551
225FADFADFADFAD(chain B and (resseq 1:4 or (resid 5 and (name...BJ901
31METMETALAALA(chain C and (resseq 1:4 or (resid 5 and (name...CD1 - 331 - 33
32TYRTYRGLUGLU(chain C and (resseq 1:4 or (resid 5 and (name...CD36 - 6036 - 60
33ARGARGVALVAL(chain C and (resseq 1:4 or (resid 5 and (name...CD67 - 9967 - 99
34ASNASNILEILE(chain C and (resseq 1:4 or (resid 5 and (name...CD101 - 128101 - 128
35ALAALAGLUGLU(chain C and (resseq 1:4 or (resid 5 and (name...CD130 - 143130 - 143
36ILEILEGLYGLY(chain C and (resseq 1:4 or (resid 5 and (name...CD145 - 152145 - 152
37LYSLYSMETMET(chain C and (resseq 1:4 or (resid 5 and (name...CD155 - 177155 - 177
38VALVALASPASP(chain C and (resseq 1:4 or (resid 5 and (name...CD179 - 194179 - 194
39GLUGLUSERSER(chain C and (resseq 1:4 or (resid 5 and (name...CD196 - 223196 - 223
310ARGARGVALVAL(chain C and (resseq 1:4 or (resid 5 and (name...CD229 - 231229 - 231
311ASNASNILEILE(chain C and (resseq 1:4 or (resid 5 and (name...CD234 - 249234 - 249
312PROPROGLUGLU(chain C and (resseq 1:4 or (resid 5 and (name...CD251 - 257251 - 257
313ALAALAILEILE(chain C and (resseq 1:4 or (resid 5 and (name...CD259 - 263259 - 263
314THRTHRGLYGLY(chain C and (resseq 1:4 or (resid 5 and (name...CD266 - 321266 - 321
315ALAALATRPTRP(chain C and (resseq 1:4 or (resid 5 and (name...CD324 - 390324 - 390
316VALVALPHEPHE(chain C and (resseq 1:4 or (resid 5 and (name...CD392 - 462392 - 462
317ILEILESERSER(chain C and (resseq 1:4 or (resid 5 and (name...CD473 - 480473 - 480
318GLUGLUGLUGLU(chain C and (resseq 1:4 or (resid 5 and (name...CD483483
319LYSLYSARGARG(chain C and (resseq 1:4 or (resid 5 and (name...CD493 - 503493 - 503
320ARGARGLEULEU(chain C and (resseq 1:4 or (resid 5 and (name...CD505 - 506505 - 506
321GLUGLUPROPRO(chain C and (resseq 1:4 or (resid 5 and (name...CD508 - 510508 - 510
322LYSLYSLEULEU(chain C and (resseq 1:4 or (resid 5 and (name...CD513 - 532513 - 532
323ALAALAPHEPHE(chain C and (resseq 1:4 or (resid 5 and (name...CD535 - 537535 - 537
324LYSLYSPHEPHE(chain C and (resseq 1:4 or (resid 5 and (name...CD539 - 551539 - 551
325FADFADFADFAD(chain C and (resseq 1:4 or (resid 5 and (name...CM901
41METMETALAALA(chain D and (resseq 1:4 or (resid 5 and (name...DA1 - 331 - 33
42TYRTYRGLUGLU(chain D and (resseq 1:4 or (resid 5 and (name...DA36 - 6036 - 60
43ARGARGVALVAL(chain D and (resseq 1:4 or (resid 5 and (name...DA67 - 9967 - 99
44ASNASNILEILE(chain D and (resseq 1:4 or (resid 5 and (name...DA101 - 128101 - 128
45ALAALAGLUGLU(chain D and (resseq 1:4 or (resid 5 and (name...DA130 - 143130 - 143
46ILEILEGLYGLY(chain D and (resseq 1:4 or (resid 5 and (name...DA145 - 152145 - 152
47LYSLYSMETMET(chain D and (resseq 1:4 or (resid 5 and (name...DA155 - 177155 - 177
48VALVALASPASP(chain D and (resseq 1:4 or (resid 5 and (name...DA179 - 194179 - 194
49GLUGLUSERSER(chain D and (resseq 1:4 or (resid 5 and (name...DA196 - 223196 - 223
410ARGARGVALVAL(chain D and (resseq 1:4 or (resid 5 and (name...DA229 - 231229 - 231
411ASNASNILEILE(chain D and (resseq 1:4 or (resid 5 and (name...DA234 - 249234 - 249
412PROPROGLUGLU(chain D and (resseq 1:4 or (resid 5 and (name...DA251 - 257251 - 257
413ALAALAILEILE(chain D and (resseq 1:4 or (resid 5 and (name...DA259 - 263259 - 263
414THRTHRGLYGLY(chain D and (resseq 1:4 or (resid 5 and (name...DA266 - 321266 - 321
415ALAALATRPTRP(chain D and (resseq 1:4 or (resid 5 and (name...DA324 - 390324 - 390
416VALVALPHEPHE(chain D and (resseq 1:4 or (resid 5 and (name...DA392 - 462392 - 462
417ILEILESERSER(chain D and (resseq 1:4 or (resid 5 and (name...DA473 - 480473 - 480
418GLUGLUGLUGLU(chain D and (resseq 1:4 or (resid 5 and (name...DA483483
419LYSLYSARGARG(chain D and (resseq 1:4 or (resid 5 and (name...DA493 - 503493 - 503
420ARGARGLEULEU(chain D and (resseq 1:4 or (resid 5 and (name...DA505 - 506505 - 506
421GLUGLUPROPRO(chain D and (resseq 1:4 or (resid 5 and (name...DA508 - 510508 - 510
422LYSLYSLEULEU(chain D and (resseq 1:4 or (resid 5 and (name...DA513 - 532513 - 532
423ALAALAPHEPHE(chain D and (resseq 1:4 or (resid 5 and (name...DA535 - 537535 - 537
424LYSLYSPHEPHE(chain D and (resseq 1:4 or (resid 5 and (name...DA539 - 551539 - 551
425FADFADFADFAD(chain D and (resseq 1:4 or (resid 5 and (name...DE901

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要素

#1: タンパク質
NADH oxidase (NoxA-3)


分子量: 60254.062 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Archaeoglobus fulgidus DSM 4304 (古細菌)
株: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 / 遺伝子: AF_0400 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O29847
#2: 化合物
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C27H33N9O15P2 / コメント: FAD*YM
#3: 化合物
ChemComp-COA / COENZYME A / CoA


分子量: 767.534 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C21H36N7O16P3S
#4: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Ca
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 14 / 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N

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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: 2.41 Å3/Da / 溶媒含有率: 48.94 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 100-200 mM calcium acetate, 15-20% PEG 3350 (w/w), and 1 mM DTT

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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-E / 波長: 0.98 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2016年5月10日
詳細: Cryogenically-cooled single crystal Si(220) side bounce monochromator.
放射モノクロメーター: Cryogenically-cooled single crystal
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: 0.98 Å / 相対比: 1
反射解像度: 3.1→40 Å / Num. obs: 80127 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 5.2 % / Biso Wilson estimate: 58.5513273334 Å2 / Rsym value: 0.119 / Net I/σ(I): 10.3
反射 シェル解像度: 3.1→3.27 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6083 / Rsym value: 0.54

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10_2155精密化
XDSデータ削減
XDSデータスケーリング
BALBES位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4FX9

4fx9


解像度: 3.10003870577→39.4818037712 Å / SU ML: 0.313808297468 / 交差検証法: FREE R-VALUE / σ(F): 1.06887880485 / 位相誤差: 22.6307325214
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.228746674435 2782 3.48272408613 %
Rwork0.202274311858 77098 -
obs0.203188436559 79880 97.8645724857 %
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: 55.5125936023 Å2
精密化ステップサイクル: LAST / 解像度: 3.10003870577→39.4818037712 Å
タンパク質核酸リガンド溶媒全体
原子数16658 0 4 14 16676
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.023963099815616914
X-RAY DIFFRACTIONf_angle_d1.9872641866922984
X-RAY DIFFRACTIONf_chiral_restr0.2927769680122680
X-RAY DIFFRACTIONf_plane_restr0.01196898498292920
X-RAY DIFFRACTIONf_dihedral_angle_d24.69297800966121
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.15350.2959278307361470.2982326729213977X-RAY DIFFRACTION99.0869774147
3.1535-3.21080.333042308051340.2882649407043846X-RAY DIFFRACTION98.8574267263
3.2108-3.27250.2949866838241580.2746348808633886X-RAY DIFFRACTION98.802834107
3.2725-3.33930.2880127162571300.2590795845153904X-RAY DIFFRACTION98.7999020328
3.3393-3.41180.2845786049961280.2476542254993935X-RAY DIFFRACTION98.8324008757
3.4118-3.49120.2385869692851520.2476925071273719X-RAY DIFFRACTION96.1500248385
3.4912-3.57840.2674210577791310.2252106128943951X-RAY DIFFRACTION99.0295972829
3.5784-3.67510.232854294951500.2170149195593782X-RAY DIFFRACTION96.3017389175
3.6751-3.78320.2488615699041210.2098828142483835X-RAY DIFFRACTION98.3834866949
3.7832-3.90520.2151505343021480.2062139379413807X-RAY DIFFRACTION96.3928832562
3.9052-4.04460.2133235546921450.19686968353889X-RAY DIFFRACTION98.3422720624
4.0446-4.20640.2299568635931380.1829323770653855X-RAY DIFFRACTION98.7144622991
4.2064-4.39760.226213960311350.1712775720063902X-RAY DIFFRACTION98.3434835566
4.3976-4.62910.1901348904241430.1658613587743800X-RAY DIFFRACTION98.0845771144
4.6291-4.91860.1922697184271410.1651495965123907X-RAY DIFFRACTION98.2285852948
4.9186-5.29760.2036412946111360.181102494483887X-RAY DIFFRACTION98.3859134263
5.2976-5.82920.2113637694391330.2040708597153875X-RAY DIFFRACTION98.2112227395
5.8292-6.66920.2117779374781330.1975623925313814X-RAY DIFFRACTION96.9778869779
6.6692-8.38920.2072762149761420.1746770648773825X-RAY DIFFRACTION97.2303921569
8.3892-39.4850.2148034710091370.180695679673702X-RAY DIFFRACTION94.2779960707
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)
11.92368640827-0.6162384357460.2035728111710.8530125808990.3198369817842.03689994473-0.0961450741247-0.04409766785290.149170767312-0.04224239087230.02480422110470.115968298826-0.201740040377-0.1834281089510.1076161267530.412555842754-0.03361392266340.04394190214220.342956392022-0.03866788193910.414284469425-32.1510048328.8673002943203.822341323
22.79528501480.6161443746950.8668181109731.534618078870.01294452395011.81093356624-0.02098885923990.249960538192-0.4118654601040.141953767666-0.1723767154850.5291667271490.43264496546-0.1241582054660.2700034913390.399344684756-0.04443608764570.09504446623130.342812990523-0.08959513043160.442053836423-26.332003974412.3535216679199.526462372
33.884694644961.44141547268-0.8701375035923.33005747081-1.114329245482.947349485950.0809573965809-0.302196957588-0.1979226300330.418163117642-0.07731581793230.02984905038240.1804529495780.05238161030180.04383477619920.3619252349120.03929371584330.03819228659370.2784998604370.008750906084570.281038255638-5.4080033910618.0493665082214.726030235
43.98674223211-0.494435591572-3.379493174212.663214444580.5532904422166.572648139740.194408000603-0.431355848967-0.4162188132730.166898849835-0.385457861434-0.08303998669760.1165494445460.186308665630.199123492180.3363274697760.0561263332035-0.03638801664180.4504583853760.01721637653620.410478625583-2.9116633982813.2861109401227.409505994
54.93323643529-0.245227313032-2.311475244171.246500030931.25141732521.790715526440.0114515621192-0.6736070702590.02610726898831.22887800769-0.2627820069160.0215394392566-0.0849414555406-0.1603646050460.1344618806640.726610083022-0.02883774380460.07229443844750.897833077793-0.100912728590.3646753696613.5813372275324.6415610308241.898718512
67.96185612401-1.14000973816-0.5709607204162.418757037721.753644653383.10219482422-0.60286838697-0.973658859708-0.4339709022780.8123864815790.254617641488-0.0162718930789-0.04420974810950.09095526194320.3575098764490.5529386259530.041006600179-0.05045635099350.7954425364360.03967954763410.4432906607740.8059753052318.2108144914234.53600616
70.002306691239410.129729735729-0.0298937182455-0.12385162234-0.1235126165111.307375121020.0901444497975-0.307255845943-0.1227596204670.4748868389360.172574691165-0.03720627852910.4353590934470.208297811746-0.02150628218280.399753596261-0.0302933001129-0.03719316098150.348218473924-0.01409798146540.4291280836812.8709138993-2.64997906454154.809418594
81.45459246363-0.235971471369-0.2239116506721.892219700221.241802752951.961871750360.03509786724760.1757431464380.0342208919282-0.110484319196-0.07090349659430.213945437915-0.0561237099561-0.22200318876-0.05610134411330.2144687034790.00348567003812-0.01674405448020.2956052003180.06329941490010.3100559814696.235630961-3.4135908801136.165223266
91.670635960010.20279748815-0.5924824974630.576238427656-0.4749675527050.807236152576-0.005283086546420.1899227293490.01293099690640.01744097554540.1132484611070.0656811021470.003764763549550.0004301675868160.04021967086410.2477707692720.00456984611066-0.03288528172030.2112610344190.0407480590250.22253274729229.14622901114.58052352746131.904556644
100.106966559059-0.5483010546721.34003569530.623495345252-1.326205284044.308270010080.1527995443641.059159516280.205301384849-0.2060390250820.04425515805710.243142913293-0.31432867216-0.1459919889160.3312832832180.3850983516150.03938892503560.02272029037560.571891803908-0.02555435217690.55942834241836.91357166593.773745268113.565366304
111.37746431502-0.0744479049907-0.5894870942290.8532966722380.6706526206652.29188087490.001222873509240.317911187237-0.0105062564453-0.136153139606-0.0565292994230.008097811534240.378088270269-0.3142666497180.03161362356310.3541685933440.02679961410140.02212236721450.570729564819-0.03835168509890.37759049197842.5180239132-5.79041524319105.223854214
120.636926736889-0.8106719391660.007317900983820.976056869985-1.115323787072.42510369787-0.07719365603740.257269953981-0.325477069248-0.4563878424250.0655117078453-0.1647002406630.504423795926-0.360073870449-0.0697196427540.394665498334-0.03558077207130.006133537930.3431823983640.002015791436380.34974349459260.4210510394-3.93758791751120.658159848
131.536914826910.291492156998-0.09290232155611.81341134255-1.262043008611.797823727350.032905378265-0.151419076138-0.264301250101-0.0418223360317-0.100780335551-0.2068068719080.1020567255620.231185795537-0.01945923510890.179863866928-0.03140530614380.02315846539020.173649617292-0.02637787918530.23745840521562.1164849557-1.16552490468139.842640599
142.11934424875-0.9291939767871.138901112830.2846520268880.02711623942342.441243806820.0625499146637-0.1947250158270.1878820108260.159883927985-0.0411805220612-0.10001609030.007241245722720.1172349481790.01521765492360.257780518318-0.008663525436430.05980925233920.1603335845120.006672711192180.25856025325436.54406728744.04787368356147.521352808
154.26747668959-1.026845965273.134762922823.10005108313-3.36539408146.716778293050.133786578452-0.575512818590.01067222976160.8058418060930.0471757435077-0.516203115278-0.1799059246550.4918410714230.06720112920890.340092196645-0.0211183640798-0.03984542129960.385983499993-0.04577441577060.32764071209934.94162298746.4935576497161.880123233
161.50932531118-0.1221645265520.9498963855170.888263501132-0.9220279600471.186252393090.18049805939-0.688118855583-0.1453820718140.430637656688-0.2443736972540.05909607269830.2047000246640.146083573991-0.1228391422260.3530942379930.02466485767080.07582212939760.5400334640890.04421239421610.3658253602128.3502461627-4.14809394751172.804487544
173.35995279269-2.17445611965-0.6712044186682.359411931610.5113541381080.6311438378210.680829923755-0.438238479706-0.321018217086-0.232542864856-0.292752209626-0.499029878259-0.05492429547050.4169302087940.121644456320.4470980291160.0139867207358-0.02517178172960.5243168543090.009370739436490.28551798253730.13352732082.19518475547166.436656136
180.4311612998480.109610869806-0.1434760664180.997309799034-1.014362961671.51494159034-0.0666507837473-0.3196556630570.2112264261780.1766016742950.0828727939822-0.0750796047588-0.1168947554020.104102396345-0.06089426711120.3792591336620.0567561663903-0.01755720250370.4412892369230.01621621896520.40113497452723.960278709125.3351393632215.792122518
191.91122689169-0.100850959516-0.3994800404671.71906309937-0.7253400655881.07962514732-0.008350587854520.1451467998340.0295905684288-0.136649693056-0.00319687041662-0.2043910001760.02997018644480.206881506788-0.0597315335090.3560069271860.02537261454950.0495444154630.287343423292-0.09565566002260.27470091662120.885241108424.1327740404197.639477023
202.010696225310.1192427060180.557586463590.6829276730450.02970157612580.690910627866-0.006066634649880.159330506394-0.124636035817-0.06801476049060.04392705795260.111825727765-0.01049285883550.084883157216-0.1536160103630.43597527262-0.02071526579350.05869736069260.316201214499-0.01982293016090.303793007565-1.1084734260119.4689755672197.682092028
210.1279909495580.374128535494-0.06988150616640.463661953367-0.01904196288650.7044101755340.08242397180260.4010657914830.4690473989740.0991587996192-0.291619359640.1167796243070.0730588813355-0.0271009561653-0.1192451055480.8808760724250.0180044920246-0.05536825004660.8464489916380.08708758124660.54161920151-10.482636654532.024678054172.655210404
220.0908748684644-0.1784864291960.1908128641230.113835690697-0.1587487158450.0555559761112-0.2362374516810.439507682505-0.1405680221890.526389396534-0.2290731937270.231914683287-0.06045063086060.08209582967887.65784837033E-80.442400554367-0.0216104976079-0.05928836295230.7753590989120.06135753298010.292149219163-10.016783576127.0259366961176.189609242
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 253 )
2X-RAY DIFFRACTION2chain 'D' and (resid 254 through 340 )
3X-RAY DIFFRACTION3chain 'D' and (resid 341 through 439 )
4X-RAY DIFFRACTION4chain 'D' and (resid 440 through 472 )
5X-RAY DIFFRACTION5chain 'D' and (resid 473 through 513 )
6X-RAY DIFFRACTION6chain 'D' and (resid 514 through 551 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 76 )
8X-RAY DIFFRACTION8chain 'A' and (resid 77 through 284 )
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 439 )
10X-RAY DIFFRACTION10chain 'A' and (resid 440 through 472 )
11X-RAY DIFFRACTION11chain 'A' and (resid 473 through 551 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 340 )
14X-RAY DIFFRACTION14chain 'B' and (resid 341 through 439 )
15X-RAY DIFFRACTION15chain 'B' and (resid 440 through 473 )
16X-RAY DIFFRACTION16chain 'B' and (resid 474 through 522 )
17X-RAY DIFFRACTION17chain 'B' and (resid 523 through 551 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 175 )
19X-RAY DIFFRACTION19chain 'C' and (resid 176 through 304 )
20X-RAY DIFFRACTION20chain 'C' and (resid 305 through 452 )
21X-RAY DIFFRACTION21chain 'C' and (resid 453 through 513 )
22X-RAY DIFFRACTION22chain 'C' and (resid 514 through 551 )

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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://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