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- PDB-5mu0: ACC1 Fab fragment in complex with citrullinated C1 epitope of CII... -

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基本情報

登録情報
データベース: PDB / ID: 5mu0
タイトルACC1 Fab fragment in complex with citrullinated C1 epitope of CII (IA03)
要素
  • IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
  • heavy chain of ACC1 antibody Fab fragment
  • light chain of ACC1 antibody Fab fragment
キーワードIMMUNE SYSTEM / anti-citrullinated protein antibody (ACPA) Fab fragment collagen type II citrullinated C1 epitope
機能・相同性
機能・相同性情報


Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / Collagen degradation ...Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / Collagen degradation / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / embryonic skeletal joint morphogenesis / otic vesicle development / ECM proteoglycans / proteoglycan metabolic process / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Integrin cell surface interactions / notochord development / limb bud formation / cartilage development involved in endochondral bone morphogenesis / limb morphogenesis / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / endochondral ossification / collagen trimer / collagen fibril organization / cartilage development / skeletal system morphogenesis / proteoglycan binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / inner ear morphogenesis / cartilage condensation / roof of mouth development / inner ear development / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / extracellular matrix / ossification / skeletal system development / central nervous system development / sensory perception of sound / bone development / regulation of gene expression / collagen-containing extracellular matrix / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / cytoplasm
類似検索 - 分子機能
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Collagen alpha-1(II) chain
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å
データ登録者Dobritzsch, D. / Holmdahl, R. / Ge, C.
資金援助 スウェーデン, 8件
組織認可番号国
Swedish Foundation for Strategic ResearchRBa08-0047 スウェーデン
Swedish Foundation for Strategic ResearchRB13-015 スウェーデン
Knut and Alice Wallenberg FoundationKAW 2010.0148 スウェーデン
Swedish Research CouncilK2009-75SX-21029-01-3 スウェーデン
Swedish Research CouncilK2012-75SX-22072-01-3 スウェーデン
Swedish Research CouncilK2011-52X-07931-25-5 スウェーデン
Swedish Research Council2015-02662 スウェーデン
European UnionIMI 115142
引用ジャーナル: JCI Insight / 年: 2017
タイトル: Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.
著者: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. / ...著者: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. / Burkhardt, H. / Dobritzsch, D. / Holmdahl, R.
履歴
登録2017年1月11日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年7月19日Provider: repository / タイプ: Initial release
改定 1.12017年9月13日Group: Author supporting evidence / Refinement description / カテゴリ: pdbx_audit_support / refine_hist
Item: _pdbx_audit_support.funding_organization / _refine_hist.d_res_low
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _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
改定 2.12024年1月17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: heavy chain of ACC1 antibody Fab fragment
B: light chain of ACC1 antibody Fab fragment
C: heavy chain of ACC1 antibody Fab fragment
D: light chain of ACC1 antibody Fab fragment
E: heavy chain of ACC1 antibody Fab fragment
F: light chain of ACC1 antibody Fab fragment
G: heavy chain of ACC1 antibody Fab fragment
H: light chain of ACC1 antibody Fab fragment
I: heavy chain of ACC1 antibody Fab fragment
J: light chain of ACC1 antibody Fab fragment
K: heavy chain of ACC1 antibody Fab fragment
L: light chain of ACC1 antibody Fab fragment
M: heavy chain of ACC1 antibody Fab fragment
N: light chain of ACC1 antibody Fab fragment
O: heavy chain of ACC1 antibody Fab fragment
P: light chain of ACC1 antibody Fab fragment
Q: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
R: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
S: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
T: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
U: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
V: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
W: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
X: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)390,03324
ポリマ－390,03324
非ポリマー00
水1,44180
1
A: heavy chain of ACC1 antibody Fab fragment
B: light chain of ACC1 antibody Fab fragment
Q: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)48,7543
ポリマ－48,7543
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-26 kcal/mol
Surface area19580 Å2
手法PISA
2
C: heavy chain of ACC1 antibody Fab fragment
D: light chain of ACC1 antibody Fab fragment
R: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)48,7543
ポリマ－48,7543
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-28 kcal/mol
Surface area19510 Å2
手法PISA
3
E: heavy chain of ACC1 antibody Fab fragment
F: light chain of ACC1 antibody Fab fragment
S: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)48,7543
ポリマ－48,7543
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-26 kcal/mol
Surface area19780 Å2
手法PISA
4
G: heavy chain of ACC1 antibody Fab fragment
H: light chain of ACC1 antibody Fab fragment
T: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)48,7543
ポリマ－48,7543
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-26 kcal/mol
Surface area19710 Å2
手法PISA
5
I: heavy chain of ACC1 antibody Fab fragment
J: light chain of ACC1 antibody Fab fragment
U: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)48,7543
ポリマ－48,7543
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-26 kcal/mol
Surface area19590 Å2
手法PISA
6
K: heavy chain of ACC1 antibody Fab fragment
L: light chain of ACC1 antibody Fab fragment
V: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)48,7543
ポリマ－48,7543
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-25 kcal/mol
Surface area19760 Å2
手法PISA
7
M: heavy chain of ACC1 antibody Fab fragment
N: light chain of ACC1 antibody Fab fragment
W: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)48,7543
ポリマ－48,7543
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-27 kcal/mol
Surface area19320 Å2
手法PISA
8
O: heavy chain of ACC1 antibody Fab fragment
P: light chain of ACC1 antibody Fab fragment
X: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


分子量 (理論値)分子数
合計 (水以外)48,7543
ポリマ－48,7543
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-24 kcal/mol
Surface area19430 Å2
手法PISA
単位格子
Length a, b, c (Å)87.147, 93.052, 121.751
Angle α, β, γ (deg.)92.75, 106.45, 104.37
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
11A
21C
12A
22E
13A
23G
14A
24I
15A
25K
16A
26M
17A
27O
18B
28D
19B
29F
110B
210H
111B
211J
112B
212L
113B
213N
114B
214P
115C
215E
116C
216G
117C
217I
118C
218K
119C
219M
120C
220O
121D
221F
122D
222H
123D
223J
124D
224L
125D
225N
126D
226P
127E
227G
128E
228I
129E
229K
130E
230M
131E
231O
132F
232H
133F
233J
134F
234L
135F
235N
136F
236P
137G
237I
138G
238K
139G
239M
140G
240O
141H
241J
142H
242L
143H
243N
144H
244P
145I
245K
146I
246M
147I
247O
148J
248L
149J
249N
150J
250P
151K
251M
152K
252O
153L
253N
154L
254P
155M
255O
156N
256P

NCSドメイン領域:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUAA1 - 2141 - 214
21GLUGLUGLUGLUCC1 - 2141 - 214
12GLUGLUGLYGLYAA1 - 2171 - 217
22GLUGLUGLYGLYEE1 - 2171 - 217
13GLUGLUGLYGLYAA1 - 2171 - 217
23GLUGLUGLYGLYGG1 - 2171 - 217
14GLUGLUGLYGLYAA1 - 2171 - 217
24GLUGLUGLYGLYII1 - 2171 - 217
15GLUGLUARGARGAA1 - 2161 - 216
25GLUGLUARGARGKK1 - 2161 - 216
16GLUGLUGLUGLUAA1 - 2141 - 214
26GLUGLUGLUGLUMM1 - 2141 - 214
17VALVALPROPROAA2 - 2152 - 215
27VALVALPROPROOO2 - 2152 - 215
18ASPASPGLUGLUBB1 - 2171 - 217
28ASPASPGLUGLUDD1 - 2171 - 217
19ASPASPARGARGBB1 - 2151 - 215
29ASPASPARGARGFF1 - 2151 - 215
110ASPASPGLUGLUBB1 - 2171 - 217
210ASPASPGLUGLUHH1 - 2171 - 217
111ASPASPGLUGLUBB1 - 2171 - 217
211ASPASPGLUGLUJJ1 - 2171 - 217
112ASPASPGLUGLUBB1 - 2171 - 217
212ASPASPGLUGLULL1 - 2171 - 217
113ASPASPASNASNBB1 - 2141 - 214
213ASPASPASNASNNN1 - 2141 - 214
114ASPASPARGARGBB1 - 2151 - 215
214ASPASPARGARGPP1 - 2151 - 215
115GLUGLUPROPROCC1 - 2151 - 215
215GLUGLUPROPROEE1 - 2151 - 215
116GLUGLUGLUGLUCC1 - 2141 - 214
216GLUGLUGLUGLUGG1 - 2141 - 214
117GLUGLUGLUGLUCC1 - 2141 - 214
217GLUGLUGLUGLUII1 - 2141 - 214
118GLUGLUGLUGLUCC1 - 2141 - 214
218GLUGLUGLUGLUKK1 - 2141 - 214
119GLUGLUPROPROCC1 - 2151 - 215
219GLUGLUPROPROMM1 - 2151 - 215
120VALVALPROPROCC2 - 2152 - 215
220VALVALPROPROOO2 - 2152 - 215
121ASPASPARGARGDD1 - 2151 - 215
221ASPASPARGARGFF1 - 2151 - 215
122ASPASPGLUGLUDD1 - 2171 - 217
222ASPASPGLUGLUHH1 - 2171 - 217
123ASPASPGLUGLUDD1 - 2171 - 217
223ASPASPGLUGLUJJ1 - 2171 - 217
124ASPASPGLUGLUDD1 - 2171 - 217
224ASPASPGLUGLULL1 - 2171 - 217
125ASPASPASNASNDD1 - 2141 - 214
225ASPASPASNASNNN1 - 2141 - 214
126ASPASPARGARGDD1 - 2151 - 215
226ASPASPARGARGPP1 - 2151 - 215
127GLUGLUGLYGLYEE1 - 2171 - 217
227GLUGLUGLYGLYGG1 - 2171 - 217
128GLUGLUPROPROEE1 - 2181 - 218
228GLUGLUPROPROII1 - 2181 - 218
129GLUGLUPROPROEE1 - 2181 - 218
229GLUGLUPROPROKK1 - 2181 - 218
130GLUGLUPROPROEE1 - 2151 - 215
230GLUGLUPROPROMM1 - 2151 - 215
131VALVALGLUGLUEE2 - 2142 - 214
231VALVALGLUGLUOO2 - 2142 - 214
132ASPASPARGARGFF1 - 2151 - 215
232ASPASPARGARGHH1 - 2151 - 215
133ASPASPARGARGFF1 - 2151 - 215
233ASPASPARGARGJJ1 - 2151 - 215
134ASPASPARGARGFF1 - 2151 - 215
234ASPASPARGARGLL1 - 2151 - 215
135ASPASPASNASNFF1 - 2141 - 214
235ASPASPASNASNNN1 - 2141 - 214
136ASPASPASNASNFF1 - 2161 - 216
236ASPASPASNASNPP1 - 2161 - 216
137GLUGLUARGARGGG1 - 2161 - 216
237GLUGLUARGARGII1 - 2161 - 216
138GLUGLUGLYGLYGG1 - 2171 - 217
238GLUGLUGLYGLYKK1 - 2171 - 217
139GLUGLUGLUGLUGG1 - 2141 - 214
239GLUGLUGLUGLUMM1 - 2141 - 214
140VALVALPROPROGG2 - 2152 - 215
240VALVALPROPROOO2 - 2152 - 215
141ASPASPGLUGLUHH1 - 2171 - 217
241ASPASPGLUGLUJJ1 - 2171 - 217
142ASPASPGLUGLUHH1 - 2171 - 217
242ASPASPGLUGLULL1 - 2171 - 217
143ASPASPASNASNHH1 - 2141 - 214
243ASPASPASNASNNN1 - 2141 - 214
144ASPASPARGARGHH1 - 2151 - 215
244ASPASPARGARGPP1 - 2151 - 215
145GLUGLUPROPROII1 - 2181 - 218
245GLUGLUPROPROKK1 - 2181 - 218
146GLUGLUGLUGLUII1 - 2141 - 214
246GLUGLUGLUGLUMM1 - 2141 - 214
147VALVALGLUGLUII2 - 2142 - 214
247VALVALGLUGLUOO2 - 2142 - 214
148ASPASPGLUGLUJJ1 - 2171 - 217
248ASPASPGLUGLULL1 - 2171 - 217
149ASPASPASNASNJJ1 - 2141 - 214
249ASPASPASNASNNN1 - 2141 - 214
150ASPASPARGARGJJ1 - 2151 - 215
250ASPASPARGARGPP1 - 2151 - 215
151GLUGLUGLUGLUKK1 - 2141 - 214
251GLUGLUGLUGLUMM1 - 2141 - 214
152VALVALPROPROKK2 - 2152 - 215
252VALVALPROPROOO2 - 2152 - 215
153ASPASPASNASNLL1 - 2141 - 214
253ASPASPASNASNNN1 - 2141 - 214
154ASPASPARGARGLL1 - 2151 - 215
254ASPASPARGARGPP1 - 2151 - 215
155VALVALPROPROMM2 - 2152 - 215
255VALVALPROPROOO2 - 2152 - 215
156ASPASPASNASNNN1 - 2141 - 214
256ASPASPASNASNPP1 - 2141 - 214

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56

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要素

#1: 抗体
heavy chain of ACC1 antibody Fab fragment


分子量: 23353.164 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: B cell hybridoma / Variant: B10.RIII.Cia5
#2: 抗体
light chain of ACC1 antibody Fab fragment


分子量: 23721.199 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: B cell hybridoma / Variant: B10.RIII.Cia5
#3: タンパク質・ペプチド
IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II / Alpha-1 type II collagen


分子量: 1679.770 Da / 分子数: 8 / 由来タイプ: 合成 / 詳細: the C-terminus is aminated / 由来: (合成) Mus musculus (ハツカネズミ) / 参照: UniProt: P28481
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 80 / 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: 2.43 Å3/Da / 溶媒含有率: 49 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: 16% (w/v) PEG 8000, 0.1 M Hepes pH 7.0

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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: Diamond / ビームライン: I03 / 波長: 0.9763 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年8月14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: 0.9763 Å / 相対比: 1
反射解像度: 2.7→78.15 Å / Num. obs: 87706 / % possible obs: 90.6 % / 冗長度: 2.9 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Net I/σ(I): 20.1
反射 シェル解像度: 2.7→2.75 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 4457 / Rpim(I) all: 0.553 / % possible all: 89.7

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0155精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2OR9

2or9


解像度: 2.7→78.15 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.896 / SU B: 49.851 / SU ML: 0.427 / 交差検証法: THROUGHOUT / ESU R Free: 0.454 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.27877 4339 5 %RANDOM
Rwork0.25212 ---
obs0.25347 82058 89.23 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 72.461 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å2-1.02 Å2-0.95 Å2
2---1.8 Å22.33 Å2
3----0.37 Å2
精密化ステップサイクル: 1 / 解像度: 2.7→78.15 Å
タンパク質核酸リガンド溶媒全体
原子数26700 0 0 80 26780
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227343
X-RAY DIFFRACTIONr_bond_other_d0.0030.0225009
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.94537130
X-RAY DIFFRACTIONr_angle_other_deg1.702357892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43853492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26824.4541071
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.747154315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.63615109
X-RAY DIFFRACTIONr_chiral_restr0.0990.24170
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02130772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026081
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1383.15114067
X-RAY DIFFRACTIONr_mcbond_other1.1383.1514066
X-RAY DIFFRACTIONr_mcangle_it1.9944.71717526
X-RAY DIFFRACTIONr_mcangle_other1.9944.71817527
X-RAY DIFFRACTIONr_scbond_it0.8473.20813276
X-RAY DIFFRACTIONr_scbond_other0.8473.20913277
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4914.77919605
X-RAY DIFFRACTIONr_long_range_B_refined3.09335.0527537
X-RAY DIFFRACTIONr_long_range_B_other3.09335.05227538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / タイプ: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-ID数Rms dev position (Å)
11A124760.07
12C124760.07
21A126700.07
22E126700.07
31A126620.06
32G126620.06
41A126300.08
42I126300.08
51A125920.07
52K125920.07
61A125280.06
62M125280.06
71A122960.08
72O122960.08
81B128820.07
82D128820.07
91B129380.05
92F129380.05
101B128620.07
102H128620.07
111B128400.07
112J128400.07
121B128220.07
122L128220.07
131B126780.08
132N126780.08
141B128000.08
142P128000.08
151C125700.07
152E125700.07
161C124960.07
162G124960.07
171C124540.08
172I124540.08
181C124900.07
182K124900.07
191C125840.07
192M125840.07
201C123280.08
202O123280.08
211D129480.06
212F129480.06
221D129000.07
222H129000.07
231D129480.07
232J129480.07
241D128720.07
242L128720.07
251D127640.07
252N127640.07
261D128920.07
262P128920.07
271E126800.07
272G126800.07
281E126800.07
282I126800.07
291E126260.08
292K126260.08
301E125600.07
302M125600.07
311E123620.08
312O123620.08
321F128940.06
322H128940.06
331F128980.06
332J128980.06
341F128580.07
342L128580.07
351F128280.07
352N128280.07
361F129980.07
362P129980.07
371G126560.07
372I126560.07
381G126180.07
382K126180.07
391G125180.07
392M125180.07
401G123580.07
402O123580.07
411H128440.08
412J128440.08
421H128540.08
422L128540.08
431H126980.07
432N126980.07
441H128580.07
442P128580.07
451I125700.08
452K125700.08
461I124600.08
462M124600.08
471I122620.08
472O122620.08
481J128280.07
482L128280.07
491J126420.08
492N126420.08
501J127640.08
502P127640.08
511K123960.08
512M123960.08
521K122420.09
522O122420.09
531L126340.08
532N126340.08
541L127960.08
542P127960.08
551M123080.09
552O123080.09
561N128000.06
562P128000.06
LS精密化 シェル解像度: 2.7→2.77 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.507 295 -
Rwork0.412 5842 -
obs--85.76 %
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)
13.4572-0.8648-0.60085.22261.64047.0138-0.2305-0.2305-0.09320.2147-0.02270.15430.1276-0.42230.25320.1133-0.11330.05590.2371-0.05470.040222.8342-9.4498-18.3049
22.751-1.5936-0.09915.8169-0.33520.29460.2161-0.1940.47940.7815-0.4806-0.020.0703-0.06310.26450.2814-0.11110.24310.4901-0.17680.39364.848413.1901-8.0265
34.1701-0.103-1.23397.3542-1.3271.6379-0.0352-0.04650.08790.0721-0.12750.7085-0.1185-0.18960.16270.1764-0.08540.12860.3118-0.22290.33051.858315.091-14.1114
44.1797-1.54210.06146.36830.33972.21730.03590.36350.25-0.2619-0.255-0.5047-0.2282-0.12430.21910.1774-0.08990.09610.2194-0.01040.162533.44498.4274-27.3123
54.3169-0.1214-2.17622.86110.15773.0745-0.0052-0.47160.42320.7255-0.29620.0125-0.1273-0.01650.30140.3028-0.06510.11330.3779-0.1750.391510.867128.4854-7.9331
61.81691.9777-0.93595.9155-2.19752.22160.10630.1236-0.0529-0.4185-0.2798-0.65150.12340.54520.17350.20560.06590.1860.3568-0.03760.235785.22325.8046-39.0705
73.27070.68080.6879.3444-1.35192.39440.0994-0.2178-0.15430.19490.11050.4750.1563-0.2002-0.20990.087-0.06790.07020.1065-0.03890.119862.759210.859-30.9065
84.2934-1.3235-2.40911.5611-0.00864.31080.27080.61810.1663-0.8017-0.3506-0.22220.31760.38270.07980.65410.0250.31960.3381-0.05850.249583.852628.9132-53.5213
92.5616-2.3795-0.41053.25581.20511.64880.26050.45560.225-0.399-0.3267-0.18620.16280.09510.06620.3438-0.11180.15480.42830.11320.263647.3718-17.9656-82.3056
102.4619-2.0792-0.42213.3570.18732.78820.15220.16970.02280.106-0.1753-0.17780.0910.11440.02310.253-0.17890.05790.2171-0.02810.155147.6344-32.1613-70.074
115.94530.8290.3982.1632-0.45424.29110.16850.2745-0.1329-0.0306-0.03930.1520.36510.0857-0.12920.339-0.02950.0430.0635-0.05390.054858.702-35.0893-54.259
126.011-1.49212.15721.696-0.68454.3497-0.13730.38170.2873-0.199-0.0966-0.27760.17480.1960.23380.293-0.14280.16970.1048-0.05720.124690.325-36.9477-47.7411
134.7365-0.05580.02321.3397-0.1931.3795-0.1104-0.4178-0.08630.1669-0.03930.2321-0.1085-0.35310.14970.2551-0.05820.12070.1647-0.08630.111267.4733-26.9529-34.8801
145.97690.1636-3.57671.4617-0.28114.00870.10370.19230.6318-0.17970.1104-0.1832-0.37330.114-0.21410.3122-0.03770.04790.147-0.0260.138494.7638-21.3496-40.0155
156.5297-1.13220.66043.4220.92714.0238-0.2103-0.45470.0961.30380.0716-0.51870.5303-0.09150.13870.5743-0.0255-0.1150.2904-0.00720.195745.5008-28.2127.1019
166.8757-0.23931.78591.9531-0.42511.9587-0.2283-0.892-0.2380.70630.20480.0671-0.0744-0.35210.02350.42050.06960.15180.33810.02970.103731.2295-31.06616.3825
1749.916827.19167.556816.51717.79649.11450.4668-0.841-0.59670.2895-0.5076-0.22390.064-0.2530.04070.4130.02310.10150.28230.12020.457313.4349-42.25899.9269
185.6282-0.1631.01592.5254-1.02972.9666-0.23810.066-0.02020.01710.16460.2027-0.0546-0.15660.07350.1871-0.01650.16020.0836-0.00750.169527.1126-26.9348-10.4403
196.3574-5.4189-0.75578.32643.76756.6863-0.10041.05890.55510.0165-0.0621-0.4957-0.29650.51140.16250.4578-0.1548-0.05870.4980.0280.32260.294127.0655-59.5747
205.45330.09696.07623.18512.802712.0073-0.08940.65630.17560.31850.0633-0.15310.78530.80230.02610.2621-0.01550.06860.2664-0.03140.106556.622518.2231-51.5225
210.2229-0.08610.01730.6802-0.0027.2127-0.07510.21830.1414-0.3540.0219-0.199-0.09261.30190.05320.4035-0.12180.14660.696-0.02050.315158.200222.6554-77.5191
227.40830.97445.4032.17861.78479.83550.1946-0.94280.150.5611-0.24060.53340.0685-1.51930.0460.2099-0.0430.22050.3315-0.05080.240937.450115.3057-59.1082
235.1931-0.8726-3.05311.80520.69015.354-0.11680.1258-0.3936-0.2961-0.004-0.11670.54190.71870.12070.37650.02860.08920.4918-0.01090.142148.934310.5305-92.6691
243.5223-0.2898-1.92438.2026-0.36846.1157-0.2785-0.18190.1316-0.0326-0.11350.2921-0.471-0.27650.3920.2048-0.081-0.03190.3110.03430.339936.500527.4271-7.737
250.5033-0.6180.12613.10253.32225.6405-0.2878-0.36410.10940.75030.18070.06390.0044-0.40380.10710.75690.00740.12710.51360.13580.631837.101934.695414.044
264.7205-0.43083.62792.5888-0.40276.7077-0.07930.4276-0.2144-0.46890.4178-1.4253-0.27820.93-0.33850.1214-0.09330.31930.4157-0.17130.944957.633825.2475-3.6738
271.22450.02610.27311.64780.07273.45280.1047-0.4263-0.19261.20740.1975-0.0934-0.09830.0235-0.30220.92880.08550.06380.6532-0.00230.658749.07228.495430.5771
281.65310.60461.65326.9043-0.33355.3351-0.5076-0.68460.67941.29790.5629-0.0738-0.5664-0.756-0.05530.6340.3346-0.18380.7244-0.03220.943360.63629.636719.0187
294.21913.2509-0.62922.5801-0.30044.27060.9472-0.19860.36930.9175-0.08720.2422-1.2969-0.9612-0.861.3670.38820.30471.3130.26930.662855.0976-11.93440.1853
304.9861-3.13311.70588.8946-2.57653.98590.18670.8450.4765-0.5259-0.3048-1.06990.12040.76870.11810.213-0.10180.0470.57850.1870.504769.2984-9.17948.8828
316.2494-0.9296-4.4271.59891.65844.4524-0.05420.47470.09620.51490.0320.44030.08-1.0430.02220.81310.15950.08711.12240.37350.544349.2725-25.667933.8395
321.7727-0.9938-2.706817.0839-2.73685.23390.03220.17820.0675-0.37760.0558-0.01510.0759-0.3063-0.0880.19740.00080.1320.3554-0.01010.149633.5842-8.1051-31.9189
330.1027-0.02590.22120.0188-0.03610.57360.07370.0429-0.12440.0310.02390.08460.14330.1882-0.09750.4409-0.0060.05170.36860.05970.524465.1816-3.5356-22.2479
341.09982.5439-0.93877.9292-2.26280.806-0.1087-0.01040.20590.59650.26440.4640.0555-0.0049-0.15570.38810.0247-0.01910.40240.00860.543426.5904-8.0348-66.3412
356.94380.99258.40140.17031.204210.3473-0.1514-1.27340.0402-0.0262-0.01920.0392-0.4047-1.56290.17060.49370.08180.13461.10320.17860.412846.4736-34.581-41.718
361.00280.35890.59330.13160.21070.35870.011-0.1345-0.02790.012-0.0243-0.0431-0.0389-0.05360.01330.3802-0.06030.00750.5012-0.02010.616959.1044-29.1769-5.3285
373.6056-2.44087.32489.2649-12.38922.1330.3862-1.28630.19-0.14290.05770.72470.6638-1.8229-0.4440.32880.01840.06040.652-0.1760.443844.327523.5229-45.9438
388.8051-0.9505-0.0499.444610.009210.72450.68681.5671-0.09391.5047-0.3695-0.27151.6336-0.1735-0.31730.6205-0.09320.11080.54850.05360.317349.062527.272-17.6114
393.0753-1.26410.006916.33513.82530.932-0.1195-0.186-0.42690.08060.2776-0.43450.0065-0.0055-0.15810.29690.00790.02190.58110.00780.539673.83927.64968.2414
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A109 - 149
3X-RAY DIFFRACTION3A150 - 217
4X-RAY DIFFRACTION4B1 - 109
5X-RAY DIFFRACTION5B110 - 213
6X-RAY DIFFRACTION6C1 - 215
7X-RAY DIFFRACTION7D1 - 107
8X-RAY DIFFRACTION8D108 - 213
9X-RAY DIFFRACTION9E1 - 215
10X-RAY DIFFRACTION10F1 - 213
11X-RAY DIFFRACTION11G1 - 111
12X-RAY DIFFRACTION12G112 - 215
13X-RAY DIFFRACTION13H1 - 141
14X-RAY DIFFRACTION14H142 - 213
15X-RAY DIFFRACTION15I1 - 51
16X-RAY DIFFRACTION16I52 - 207
17X-RAY DIFFRACTION17I208 - 215
18X-RAY DIFFRACTION18J1 - 213
19X-RAY DIFFRACTION19K1 - 31
20X-RAY DIFFRACTION20K32 - 69
21X-RAY DIFFRACTION21K70 - 215
22X-RAY DIFFRACTION22L1 - 107
23X-RAY DIFFRACTION23L108 - 213
24X-RAY DIFFRACTION24M1 - 67
25X-RAY DIFFRACTION25M68 - 215
26X-RAY DIFFRACTION26N1 - 104
27X-RAY DIFFRACTION27N105 - 213
28X-RAY DIFFRACTION28O2 - 107
29X-RAY DIFFRACTION29O108 - 215
30X-RAY DIFFRACTION30P1 - 108
31X-RAY DIFFRACTION31P109 - 213
32X-RAY DIFFRACTION32Q3 - 13
33X-RAY DIFFRACTION33R4 - 13
34X-RAY DIFFRACTION34S4 - 13
35X-RAY DIFFRACTION35T4 - 13
36X-RAY DIFFRACTION36U4 - 13
37X-RAY DIFFRACTION37V4 - 13
38X-RAY DIFFRACTION38W5 - 13
39X-RAY DIFFRACTION39X4 - 13

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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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

+
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