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- PDB-3e1q: Crystal structure of W133F variant E. coli Bacterioferritn with iron. -

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基本情報

登録情報
データベース: PDB / ID: 3e1q
タイトルCrystal structure of W133F variant E. coli Bacterioferritn with iron.
要素BACTERIOFERRITIN
キーワードMETAL BINDING PROTEIN / W133F BACTERIOFERRITIN. RHOMBIC DODECAHEDRAL SUPERSTRUCTURE / HEME / IRON / IRON STORAGE / METAL-BINDING
機能・相同性
機能・相同性情報


iron ion sequestering activity / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...iron ion sequestering activity / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / cytosol
類似検索 - 分子機能
Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
: / PROTOPORPHYRIN IX CONTAINING FE / Bacterioferritin
類似検索 - 構成要素
生物種ESCHERICHIA COLI (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Crow, A. / Lawson, T.L. / Lewin, A. / Moore, G.R. / Le Brun, N.E.
引用ジャーナル: Biochemistry / : 2009
タイトル: Monitoring the iron status of the ferroxidase center of Escherichia coli bacterioferritin using fluorescence spectroscopy.
著者: Lawson, T.L. / Crow, A. / Lewin, A. / Yasmin, S. / Moore, G.R. / Le Brun, N.E.
履歴
登録2008年8月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02009年8月18日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22021年10月20日Group: Database references / Derived calculations
カテゴリ: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.32023年8月30日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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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: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)228,32458
ポリマ-221,74812
非ポリマー6,57646
7,800433
1
A: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
ヘテロ分子

A: BACTERIOFERRITIN
B: BACTERIOFERRITIN
C: BACTERIOFERRITIN
D: BACTERIOFERRITIN
E: BACTERIOFERRITIN
F: BACTERIOFERRITIN
G: BACTERIOFERRITIN
H: BACTERIOFERRITIN
I: BACTERIOFERRITIN
J: BACTERIOFERRITIN
K: BACTERIOFERRITIN
L: BACTERIOFERRITIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)456,648116
ポリマ-443,49624
非ポリマー13,15292
43224
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area102260 Å2
ΔGint-1607 kcal/mol
Surface area131550 Å2
手法PISA
単位格子
Length a, b, c (Å)207.659, 207.659, 142.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDモデル要素
11F-333-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131A
141B
151C
161D
171E
181F
191G
201H
211I
221J
231K
241L
12B
22A
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
132B
142A
152C
162D
172E
182F
192G
202H
212I
222J
232K
242L
13C
23A
33B
43D
53E
63F
73G
83H
93I
103J
113K
123L
133C
143A
153B
163D
173E
183F
193G
203H
213I
223J
233K
243L
14D
24A
34B
44C
54E
64F
74G
84H
94I
104J
114K
124L
134D
144A
154B
164C
174E
184F
194G
204H
214I
224J
234K
244L
15E
25A
35B
45C
55D
65F
75G
85H
95I
105J
115K
125L
135E
145A
155B
165C
175D
185F
195G
205H
215I
225J
235K
245L
16F
26A
36B
46C
56D
66E
76G
86H
96I
106J
116K
126L
136F
146A
156B
166C
176D
186E
196G
206H
216I
226J
236K
246L
17G
27A
37B
47C
57D
67E
77F
87H
97I
107J
117K
127L
137G
147A
157B
167C
177D
187E
197F
207H
217I
227J
237K
247L
18H
28A
38B
48C
58D
68E
78F
88G
98I
108J
118K
128L
138H
148A
158B
168C
178D
188E
198F
208G
218I
228J
238K
248L
19I
29A
39B
49C
59D
69E
79F
89G
99H
109J
119K
129L
139I
149A
159B
169C
179D
189E
199F
209G
219H
229J
239K
249L
110J
210A
310B
410C
510D
610E
710F
810G
910H
1010I
1110K
1210L
1310J
1410A
1510B
1610C
1710D
1810E
1910F
2010G
2110H
2210I
2310K
2410L
111K
211A
311B
411C
511D
611E
711F
811G
911H
1011I
1111J
1211L
1311K
1411A
1511B
1611C
1711D
1811E
1911F
2011G
2111H
2211I
2311J
2411L
112L
212A
312B
412C
512D
612E
712F
812G
912H
1012I
1112J
1212K
1312L
1412A
1512B
1612C
1712D
1812E
1912F
2012G
2112H
2212I
2312J
2412K
113A
213D
313F
413G
513I
613L
114D
214A
314F
414G
514I
614L
115F
215A
315D
415G
515I
615L
116G
216A
316D
416F
516J
616L
117I
217A
317D
417F
517G
617I
118L
218A
318D
418F
518G
618I

NCSドメイン領域:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLYGLYAA1 - 1581 - 158
211METMETGLYGLYBB1 - 1581 - 158
311METMETGLYGLYCC1 - 1581 - 158
411METMETGLYGLYDD1 - 1581 - 158
511METMETGLYGLYEE1 - 1581 - 158
611METMETGLYGLYFF1 - 1581 - 158
711METMETGLYGLYGG1 - 1581 - 158
811METMETGLYGLYHH1 - 1581 - 158
911METMETGLYGLYII1 - 1581 - 158
1011METMETGLYGLYJJ1 - 1581 - 158
1111METMETGLYGLYKK1 - 1581 - 158
1211METMETGLYGLYLL1 - 1581 - 158
1321SO4SO4FE2FE2AM - O250 - 301
1421SO4SO4FE2FE2BR - T250 - 301
1521SO4SO4FE2FE2CV - X250 - 301
1621SO4SO4FE2FE2DY - AA250 - 301
1721SO4SO4FE2FE2ECA - EA250 - 301
1821SO4SO4FE2FE2FFA - HA250 - 301
1921SO4SO4FE2FE2GKA - MA250 - 301
2021SO4SO4FE2FE2HPA - RA250 - 301
2121SO4SO4FE2FE2ISA - UA250 - 301
2221SO4SO4FE2FE2JWA - YA250 - 301
2321SO4SO4FE2FE2KZA - BB250 - 301
2421SO4SO4FE2FE2LCB - EB250 - 301
112METMETGLYGLYBB1 - 1581 - 158
212METMETGLYGLYAA1 - 1581 - 158
312METMETGLYGLYCC1 - 1581 - 158
412METMETGLYGLYDD1 - 1581 - 158
512METMETGLYGLYEE1 - 1581 - 158
612METMETGLYGLYFF1 - 1581 - 158
712METMETGLYGLYGG1 - 1581 - 158
812METMETGLYGLYHH1 - 1581 - 158
912METMETGLYGLYII1 - 1581 - 158
1012METMETGLYGLYJJ1 - 1581 - 158
1112METMETGLYGLYKK1 - 1581 - 158
1212METMETGLYGLYLL1 - 1581 - 158
1322SO4SO4FE2FE2BR - T250 - 301
1422SO4SO4FE2FE2AM - O250 - 301
1522SO4SO4FE2FE2CV - X250 - 301
1622SO4SO4FE2FE2DY - AA250 - 301
1722SO4SO4FE2FE2ECA - EA250 - 301
1822SO4SO4FE2FE2FFA - HA250 - 301
1922SO4SO4FE2FE2GKA - MA250 - 301
2022SO4SO4FE2FE2HPA - RA250 - 301
2122SO4SO4FE2FE2ISA - UA250 - 301
2222SO4SO4FE2FE2JWA - YA250 - 301
2322SO4SO4FE2FE2KZA - BB250 - 301
2422SO4SO4FE2FE2LCB - EB250 - 301
113METMETGLYGLYCC1 - 1581 - 158
213METMETGLYGLYAA1 - 1581 - 158
313METMETGLYGLYBB1 - 1581 - 158
413METMETGLYGLYDD1 - 1581 - 158
513METMETGLYGLYEE1 - 1581 - 158
613METMETGLYGLYFF1 - 1581 - 158
713METMETGLYGLYGG1 - 1581 - 158
813METMETGLYGLYHH1 - 1581 - 158
913METMETGLYGLYII1 - 1581 - 158
1013METMETGLYGLYJJ1 - 1581 - 158
1113METMETGLYGLYKK1 - 1581 - 158
1213METMETGLYGLYLL1 - 1581 - 158
1323SO4SO4FE2FE2CV - X250 - 301
1423SO4SO4FE2FE2AM - O250 - 301
1523SO4SO4FE2FE2BR - T250 - 301
1623SO4SO4FE2FE2DY - AA250 - 301
1723SO4SO4FE2FE2ECA - EA250 - 301
1823SO4SO4FE2FE2FFA - HA250 - 301
1923SO4SO4FE2FE2GKA - MA250 - 301
2023SO4SO4FE2FE2HPA - RA250 - 301
2123SO4SO4FE2FE2ISA - UA250 - 301
2223SO4SO4FE2FE2JWA - YA250 - 301
2323SO4SO4FE2FE2KZA - BB250 - 301
2423SO4SO4FE2FE2LCB - EB250 - 301
114METMETGLYGLYDD1 - 1581 - 158
214METMETGLYGLYAA1 - 1581 - 158
314METMETGLYGLYBB1 - 1581 - 158
414METMETGLYGLYCC1 - 1581 - 158
514METMETGLYGLYEE1 - 1581 - 158
614METMETGLYGLYFF1 - 1581 - 158
714METMETGLYGLYGG1 - 1581 - 158
814METMETGLYGLYHH1 - 1581 - 158
914METMETGLYGLYII1 - 1581 - 158
1014METMETGLYGLYJJ1 - 1581 - 158
1114METMETGLYGLYKK1 - 1581 - 158
1214METMETGLYGLYLL1 - 1581 - 158
1324SO4SO4FE2FE2DY - AA250 - 301
1424SO4SO4FE2FE2AM - O250 - 301
1524SO4SO4FE2FE2BR - T250 - 301
1624SO4SO4FE2FE2CV - X250 - 301
1724SO4SO4FE2FE2ECA - EA250 - 301
1824SO4SO4FE2FE2FFA - HA250 - 301
1924SO4SO4FE2FE2GKA - MA250 - 301
2024SO4SO4FE2FE2HPA - RA250 - 301
2124SO4SO4FE2FE2ISA - UA250 - 301
2224SO4SO4FE2FE2JWA - YA250 - 301
2324SO4SO4FE2FE2KZA - BB250 - 301
2424SO4SO4FE2FE2LCB - EB250 - 301
115METMETGLYGLYEE1 - 1581 - 158
215METMETGLYGLYAA1 - 1581 - 158
315METMETGLYGLYBB1 - 1581 - 158
415METMETGLYGLYCC1 - 1581 - 158
515METMETGLYGLYDD1 - 1581 - 158
615METMETGLYGLYFF1 - 1581 - 158
715METMETGLYGLYGG1 - 1581 - 158
815METMETGLYGLYHH1 - 1581 - 158
915METMETGLYGLYII1 - 1581 - 158
1015METMETGLYGLYJJ1 - 1581 - 158
1115METMETGLYGLYKK1 - 1581 - 158
1215METMETGLYGLYLL1 - 1581 - 158
1325SO4SO4FE2FE2ECA - EA250 - 301
1425SO4SO4FE2FE2AM - O250 - 301
1525SO4SO4FE2FE2BR - T250 - 301
1625SO4SO4FE2FE2CV - X250 - 301
1725SO4SO4FE2FE2DY - AA250 - 301
1825SO4SO4FE2FE2FFA - HA250 - 301
1925SO4SO4FE2FE2GKA - MA250 - 301
2025SO4SO4FE2FE2HPA - RA250 - 301
2125SO4SO4FE2FE2ISA - UA250 - 301
2225SO4SO4FE2FE2JWA - YA250 - 301
2325SO4SO4FE2FE2KZA - BB250 - 301
2425SO4SO4FE2FE2LCB - EB250 - 301
116METMETGLYGLYFF1 - 1581 - 158
216METMETGLYGLYAA1 - 1581 - 158
316METMETGLYGLYBB1 - 1581 - 158
416METMETGLYGLYCC1 - 1581 - 158
516METMETGLYGLYDD1 - 1581 - 158
616METMETGLYGLYEE1 - 1581 - 158
716METMETGLYGLYGG1 - 1581 - 158
816METMETGLYGLYHH1 - 1581 - 158
916METMETGLYGLYII1 - 1581 - 158
1016METMETGLYGLYJJ1 - 1581 - 158
1116METMETGLYGLYKK1 - 1581 - 158
1216METMETGLYGLYLL1 - 1581 - 158
1326SO4SO4FE2FE2FFA - HA250 - 301
1426SO4SO4FE2FE2AM - O250 - 301
1526SO4SO4FE2FE2BR - T250 - 301
1626SO4SO4FE2FE2CV - X250 - 301
1726SO4SO4FE2FE2DY - AA250 - 301
1826SO4SO4FE2FE2ECA - EA250 - 301
1926SO4SO4FE2FE2GKA - MA250 - 301
2026SO4SO4FE2FE2HPA - RA250 - 301
2126SO4SO4FE2FE2ISA - UA250 - 301
2226SO4SO4FE2FE2JWA - YA250 - 301
2326SO4SO4FE2FE2KZA - BB250 - 301
2426SO4SO4FE2FE2LCB - EB250 - 301
117METMETGLYGLYGG1 - 1581 - 158
217METMETGLYGLYAA1 - 1581 - 158
317METMETGLYGLYBB1 - 1581 - 158
417METMETGLYGLYCC1 - 1581 - 158
517METMETGLYGLYDD1 - 1581 - 158
617METMETGLYGLYEE1 - 1581 - 158
717METMETGLYGLYFF1 - 1581 - 158
817METMETGLYGLYHH1 - 1581 - 158
917METMETGLYGLYII1 - 1581 - 158
1017METMETGLYGLYJJ1 - 1581 - 158
1117METMETGLYGLYKK1 - 1581 - 158
1217METMETGLYGLYLL1 - 1581 - 158
1327SO4SO4FE2FE2GKA - MA250 - 301
1427SO4SO4FE2FE2AM - O250 - 301
1527SO4SO4FE2FE2BR - T250 - 301
1627SO4SO4FE2FE2CV - X250 - 301
1727SO4SO4FE2FE2DY - AA250 - 301
1827SO4SO4FE2FE2ECA - EA250 - 301
1927SO4SO4FE2FE2FFA - HA250 - 301
2027SO4SO4FE2FE2HPA - RA250 - 301
2127SO4SO4FE2FE2ISA - UA250 - 301
2227SO4SO4FE2FE2JWA - YA250 - 301
2327SO4SO4FE2FE2KZA - BB250 - 301
2427SO4SO4FE2FE2LCB - EB250 - 301
118METMETGLYGLYHH1 - 1581 - 158
218METMETGLYGLYAA1 - 1581 - 158
318METMETGLYGLYBB1 - 1581 - 158
418METMETGLYGLYCC1 - 1581 - 158
518METMETGLYGLYDD1 - 1581 - 158
618METMETGLYGLYEE1 - 1581 - 158
718METMETGLYGLYFF1 - 1581 - 158
818METMETGLYGLYGG1 - 1581 - 158
918METMETGLYGLYII1 - 1581 - 158
1018METMETGLYGLYJJ1 - 1581 - 158
1118METMETGLYGLYKK1 - 1581 - 158
1218METMETGLYGLYLL1 - 1581 - 158
1328SO4SO4FE2FE2HPA - RA250 - 301
1428SO4SO4FE2FE2AM - O250 - 301
1528SO4SO4FE2FE2BR - T250 - 301
1628SO4SO4FE2FE2CV - X250 - 301
1728SO4SO4FE2FE2DY - AA250 - 301
1828SO4SO4FE2FE2ECA - EA250 - 301
1928SO4SO4FE2FE2FFA - HA250 - 301
2028SO4SO4FE2FE2GKA - MA250 - 301
2128SO4SO4FE2FE2ISA - UA250 - 301
2228SO4SO4FE2FE2JWA - YA250 - 301
2328SO4SO4FE2FE2KZA - BB250 - 301
2428SO4SO4FE2FE2LCB - EB250 - 301
119METMETGLYGLYII1 - 1581 - 158
219METMETGLYGLYAA1 - 1581 - 158
319METMETGLYGLYBB1 - 1581 - 158
419METMETGLYGLYCC1 - 1581 - 158
519METMETGLYGLYDD1 - 1581 - 158
619METMETGLYGLYEE1 - 1581 - 158
719METMETGLYGLYFF1 - 1581 - 158
819METMETGLYGLYGG1 - 1581 - 158
919METMETGLYGLYHH1 - 1581 - 158
1019METMETGLYGLYJJ1 - 1581 - 158
1119METMETGLYGLYKK1 - 1581 - 158
1219METMETGLYGLYLL1 - 1581 - 158
1329SO4SO4FE2FE2ISA - UA250 - 301
1429SO4SO4FE2FE2AM - O250 - 301
1529SO4SO4FE2FE2BR - T250 - 301
1629SO4SO4FE2FE2CV - X250 - 301
1729SO4SO4FE2FE2DY - AA250 - 301
1829SO4SO4FE2FE2ECA - EA250 - 301
1929SO4SO4FE2FE2FFA - HA250 - 301
2029SO4SO4FE2FE2GKA - MA250 - 301
2129SO4SO4FE2FE2HPA - RA250 - 301
2229SO4SO4FE2FE2JWA - YA250 - 301
2329SO4SO4FE2FE2KZA - BB250 - 301
2429SO4SO4FE2FE2LCB - EB250 - 301
1110METMETGLYGLYJJ1 - 1581 - 158
2110METMETGLYGLYAA1 - 1581 - 158
3110METMETGLYGLYBB1 - 1581 - 158
4110METMETGLYGLYCC1 - 1581 - 158
5110METMETGLYGLYDD1 - 1581 - 158
6110METMETGLYGLYEE1 - 1581 - 158
7110METMETGLYGLYFF1 - 1581 - 158
8110METMETGLYGLYGG1 - 1581 - 158
9110METMETGLYGLYHH1 - 1581 - 158
10110METMETGLYGLYII1 - 1581 - 158
11110METMETGLYGLYKK1 - 1581 - 158
12110METMETGLYGLYLL1 - 1581 - 158
13210SO4SO4FE2FE2JWA - YA250 - 301
14210SO4SO4FE2FE2AM - O250 - 301
15210SO4SO4FE2FE2BR - T250 - 301
16210SO4SO4FE2FE2CV - X250 - 301
17210SO4SO4FE2FE2DY - AA250 - 301
18210SO4SO4FE2FE2ECA - EA250 - 301
19210SO4SO4FE2FE2FFA - HA250 - 301
20210SO4SO4FE2FE2GKA - MA250 - 301
21210SO4SO4FE2FE2HPA - RA250 - 301
22210SO4SO4FE2FE2ISA - UA250 - 301
23210SO4SO4FE2FE2KZA - BB250 - 301
24210SO4SO4FE2FE2LCB - EB250 - 301
1111METMETGLYGLYKK1 - 1581 - 158
2111METMETGLYGLYAA1 - 1581 - 158
3111METMETGLYGLYBB1 - 1581 - 158
4111METMETGLYGLYCC1 - 1581 - 158
5111METMETGLYGLYDD1 - 1581 - 158
6111METMETGLYGLYEE1 - 1581 - 158
7111METMETGLYGLYFF1 - 1581 - 158
8111METMETGLYGLYGG1 - 1581 - 158
9111METMETGLYGLYHH1 - 1581 - 158
10111METMETGLYGLYII1 - 1581 - 158
11111METMETGLYGLYJJ1 - 1581 - 158
12111METMETGLYGLYLL1 - 1581 - 158
13211SO4SO4FE2FE2KZA - BB250 - 301
14211SO4SO4FE2FE2AM - O250 - 301
15211SO4SO4FE2FE2BR - T250 - 301
16211SO4SO4FE2FE2CV - X250 - 301
17211SO4SO4FE2FE2DY - AA250 - 301
18211SO4SO4FE2FE2ECA - EA250 - 301
19211SO4SO4FE2FE2FFA - HA250 - 301
20211SO4SO4FE2FE2GKA - MA250 - 301
21211SO4SO4FE2FE2HPA - RA250 - 301
22211SO4SO4FE2FE2ISA - UA250 - 301
23211SO4SO4FE2FE2JWA - YA250 - 301
24211SO4SO4FE2FE2LCB - EB250 - 301
1112METMETGLYGLYLL1 - 1581 - 158
2112METMETGLYGLYAA1 - 1581 - 158
3112METMETGLYGLYBB1 - 1581 - 158
4112METMETGLYGLYCC1 - 1581 - 158
5112METMETGLYGLYDD1 - 1581 - 158
6112METMETGLYGLYEE1 - 1581 - 158
7112METMETGLYGLYFF1 - 1581 - 158
8112METMETGLYGLYGG1 - 1581 - 158
9112METMETGLYGLYHH1 - 1581 - 158
10112METMETGLYGLYII1 - 1581 - 158
11112METMETGLYGLYJJ1 - 1581 - 158
12112METMETGLYGLYKK1 - 1581 - 158
13212SO4SO4FE2FE2LCB - EB250 - 301
14212SO4SO4FE2FE2AM - O250 - 301
15212SO4SO4FE2FE2BR - T250 - 301
16212SO4SO4FE2FE2CV - X250 - 301
17212SO4SO4FE2FE2DY - AA250 - 301
18212SO4SO4FE2FE2ECA - EA250 - 301
19212SO4SO4FE2FE2FFA - HA250 - 301
20212SO4SO4FE2FE2GKA - MA250 - 301
21212SO4SO4FE2FE2HPA - RA250 - 301
22212SO4SO4FE2FE2ISA - UA250 - 301
23212SO4SO4FE2FE2JWA - YA250 - 301
24212SO4SO4FE2FE2KZA - BB250 - 301
1113HEMHEMHEMHEMAQ200
2113HEMHEMHEMHEMDBA200
3113HEMHEMHEMHEMFJA200
4113HEMHEMHEMHEMGOA200
5113HEMHEMHEMHEMIVA200
6113HEMHEMHEMHEMLFB200
1114HEMHEMHEMHEMDBA200
2114HEMHEMHEMHEMAQ200
3114HEMHEMHEMHEMFJA200
4114HEMHEMHEMHEMGOA200
5114HEMHEMHEMHEMIVA200
6114HEMHEMHEMHEMLFB200
1115HEMHEMHEMHEMFJA200
2115HEMHEMHEMHEMAQ200
3115HEMHEMHEMHEMDBA200
4115HEMHEMHEMHEMGOA200
5115HEMHEMHEMHEMIVA200
6115HEMHEMHEMHEMLFB200
1116HEMHEMHEMHEMGOA200
2116HEMHEMHEMHEMAQ200
3116HEMHEMHEMHEMDBA200
4116HEMHEMHEMHEMFJA200
5116HEMHEMHEMHEMIVA200
6116HEMHEMHEMHEMLFB200
1117HEMHEMHEMHEMIVA200
2117HEMHEMHEMHEMAQ200
3117HEMHEMHEMHEMDBA200
4117HEMHEMHEMHEMFJA200
5117HEMHEMHEMHEMGOA200
6117HEMHEMHEMHEMIVA200
1118HEMHEMHEMHEMLFB200
2118HEMHEMHEMHEMAQ200
3118HEMHEMHEMHEMDBA200
4118HEMHEMHEMHEMFJA200
5118HEMHEMHEMHEMGOA200
6118HEMHEMHEMHEMIVA200

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

-
要素

#1: タンパク質
BACTERIOFERRITIN / BFR / CYTOCHROME B-1 / CYTOCHROME B-557


分子量: 18478.980 Da / 分子数: 12 / 変異: W133F / 由来タイプ: 組換発現 / 由来: (組換発現) ESCHERICHIA COLI (大腸菌) / : K-12 / 遺伝子: BFR / プラスミド: PALN1 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0ABD3
#2: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 16 / 由来タイプ: 合成 / : SO4
#3: 化合物...
ChemComp-FE2 / FE (II) ION


分子量: 55.845 Da / 分子数: 24 / 由来タイプ: 合成 / : Fe
#4: 化合物
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 6 / 由来タイプ: 合成 / : C34H32FeN4O4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 433 / 由来タイプ: 天然 / : H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.47 Å3/Da / 溶媒含有率: 64.56 %
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 / pH: 5.8
詳細: BFR PROTEIN WAS PRE-LOADED WITH IRON AND THEN CRYSTALLIZED OVERNIGHT IN 1.8 M AMMONIUM SULFATE, 0.1 M MES PH 5.8. PLEASE SEE THE ORIGINAL PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING ...詳細: BFR PROTEIN WAS PRE-LOADED WITH IRON AND THEN CRYSTALLIZED OVERNIGHT IN 1.8 M AMMONIUM SULFATE, 0.1 M MES PH 5.8. PLEASE SEE THE ORIGINAL PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.80

-
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: ESRF / ビームライン: ID23-1 / 波長: 1.7429
検出器検出器: CCD / 日付: 2006年1月1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: 1.7429 Å / 相対比: 1
反射解像度: 2.595→33.32 Å / Num. obs: 93115 / % possible obs: 97.2 % / 冗長度: 13.5 % / Rsym value: 0.12 / Net I/σ(I): 19.3
反射 シェル最高解像度: 2.6 Å / 冗長度: 6.9 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.383 / % possible all: 84

-
解析

ソフトウェア
名称バージョン分類
MOLREP位相決定
REFMAC5.2.0019精密化
MOSFLMデータ削減
SCALAデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 2QPI

2qpi
PDB 未公開エントリ


解像度: 2.6→33.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.205 / SU ML: 0.197 / 交差検証法: THROUGHOUT / ESU R: 0.581 / ESU R Free: 0.306 / 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
Rfree0.263 4649 5 %COPIED AND EXTENDED FROM 2QPI
Rwork0.245 ---
obs0.246 88403 97.2 %-
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: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
精密化ステップサイクル: LAST / 解像度: 2.6→33.31 Å
タンパク質核酸リガンド溶媒全体
原子数15984 0 362 433 16779
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02116624
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5722.02322488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.59751980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88124.872936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.318153192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.80615132
X-RAY DIFFRACTIONr_chiral_restr0.1310.22340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212756
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.28008
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.211305
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2618
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.2134
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8641.59964
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.342215372
X-RAY DIFFRACTIONr_scbond_it2.19737564
X-RAY DIFFRACTIONr_scangle_it3.54.57092
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

Ens-IDDom-IDAuth asym-IDタイプRms dev position (Å)Weight position
11A1339tight positional0.010.05
12B1339tight positional0.010.05
13C1339tight positional0.010.05
14D1339tight positional0.010.05
15E1339tight positional0.010.05
16F1339tight positional0.010.05
17G1339tight positional0.010.05
18H1339tight positional0.010.05
19I1339tight positional0.010.05
110J1339tight positional0.010.05
111K1339tight positional0.010.05
112L1339tight positional0.010.05
21B1339tight positional0.010.05
22A1339tight positional0.010.05
23C1339tight positional0.010.05
24D1339tight positional0.010.05
25E1339tight positional0.010.05
26F1339tight positional0.010.05
27G1339tight positional0.010.05
28H1339tight positional0.010.05
29I1339tight positional0.010.05
210J1339tight positional0.010.05
211K1339tight positional0.010.05
212L1339tight positional0.010.05
31C1339tight positional0.010.05
32A1339tight positional0.010.05
33B1339tight positional0.010.05
34D1339tight positional0.010.05
35E1339tight positional0.010.05
36F1339tight positional0.010.05
37G1339tight positional0.010.05
38H1339tight positional0.010.05
39I1339tight positional0.010.05
310J1339tight positional0.010.05
311K1339tight positional0.010.05
312L1339tight positional0.010.05
41D1339tight positional0.010.05
42A1339tight positional0.010.05
43B1339tight positional0.010.05
44C1339tight positional0.010.05
45E1339tight positional0.010.05
46F1339tight positional0.010.05
47G1339tight positional0.010.05
48H1339tight positional0.010.05
49I1339tight positional0.010.05
410J1339tight positional0.010.05
411K1339tight positional0.010.05
412L1339tight positional0.010.05
51E1339tight positional0.010.05
52A1339tight positional0.010.05
53B1339tight positional0.010.05
54C1339tight positional0.010.05
55D1339tight positional0.010.05
56F1339tight positional0.010.05
57G1339tight positional0.010.05
58H1339tight positional0.010.05
59I1339tight positional0.010.05
510J1339tight positional0.010.05
511K1339tight positional0.010.05
512L1339tight positional0.010.05
61F1339tight positional0.010.05
62A1339tight positional0.010.05
63B1339tight positional0.010.05
64C1339tight positional0.010.05
65D1339tight positional0.010.05
66E1339tight positional0.010.05
67G1339tight positional0.010.05
68H1339tight positional0.010.05
69I1339tight positional0.010.05
610J1339tight positional0.010.05
611K1339tight positional0.010.05
612L1339tight positional0.010.05
71G1339tight positional0.010.05
72A1339tight positional0.010.05
73B1339tight positional0.010.05
74C1339tight positional0.010.05
75D1339tight positional0.010.05
76E1339tight positional0.010.05
77F1339tight positional0.010.05
78H1339tight positional0.010.05
79I1339tight positional0.010.05
710J1339tight positional0.010.05
711K1339tight positional0.010.05
712L1339tight positional0.010.05
81H1339tight positional0.010.05
82A1339tight positional0.010.05
83B1339tight positional0.010.05
84C1339tight positional0.010.05
85D1339tight positional0.010.05
86E1339tight positional0.010.05
87F1339tight positional0.010.05
88G1339tight positional0.010.05
89I1339tight positional0.010.05
810J1339tight positional0.010.05
811K1339tight positional0.010.05
812L1339tight positional0.010.05
91I1339tight positional0.010.05
92A1339tight positional0.010.05
93B1339tight positional0.010.05
94C1339tight positional0.010.05
95D1339tight positional0.010.05
96E1339tight positional0.010.05
97F1339tight positional0.010.05
98G1339tight positional0.010.05
99H1339tight positional0.010.05
910J1339tight positional0.010.05
911K1339tight positional0.010.05
912L1339tight positional0.010.05
101J1339tight positional0.010.05
102A1339tight positional0.010.05
103B1339tight positional0.010.05
104C1339tight positional0.010.05
105D1339tight positional0.010.05
106E1339tight positional0.010.05
107F1339tight positional0.010.05
108G1339tight positional0.010.05
109H1339tight positional0.010.05
1010I1339tight positional0.010.05
1011K1339tight positional0.010.05
1012L1339tight positional0.010.05
111K1339tight positional0.010.05
112A1339tight positional0.010.05
113B1339tight positional0.010.05
114C1339tight positional0.010.05
115D1339tight positional0.010.05
116E1339tight positional0.010.05
117F1339tight positional0.010.05
118G1339tight positional0.010.05
119H1339tight positional0.010.05
1110I1339tight positional0.010.05
1111J1339tight positional0.010.05
1112L1339tight positional0.010.05
121L1339tight positional0.010.05
122A1339tight positional0.010.05
123B1339tight positional0.010.05
124C1339tight positional0.010.05
125D1339tight positional0.010.05
126E1339tight positional0.010.05
127F1339tight positional0.010.05
128G1339tight positional0.010.05
129H1339tight positional0.010.05
1210I1339tight positional0.010.05
1211J1339tight positional0.010.05
1212K1339tight positional0.010.05
131B43tight positional0.010.05
132D43tight positional0.010.05
133F43tight positional0.010.05
134H43tight positional0.010.05
135J43tight positional0.010.05
136L43tight positional0.010.05
141D43tight positional0.010.05
142B43tight positional0.010.05
143F43tight positional0.010.05
144H43tight positional0.010.05
145J43tight positional0.010.05
146L43tight positional0.010.05
151F43tight positional0.010.05
152B43tight positional0.010.05
153D43tight positional0.010.05
154H43tight positional0.010.05
155J43tight positional0.010.05
156L43tight positional0.010.05
161H43tight positional0.010.05
162B43tight positional0.010.05
163D43tight positional0.010.05
164F43tight positional0.010.05
165J43tight positional0.010.05
166L43tight positional0.010.05
171J43tight positional00.05
172B43tight positional0.010.05
173D43tight positional0.010.05
174F43tight positional0.010.05
175H43tight positional0.010.05
171J43tight positional00.05
181L43tight positional0.010.05
182B43tight positional0.010.05
183D43tight positional0.010.05
184F43tight positional0.010.05
185H43tight positional0.010.05
186J43tight positional0.010.05
11A1339tight thermal0.010.5
12B1339tight thermal0.010.5
13C1339tight thermal0.010.5
14D1339tight thermal0.010.5
15E1339tight thermal0.010.5
16F1339tight thermal0.010.5
17G1339tight thermal0.010.5
18H1339tight thermal0.010.5
19I1339tight thermal0.010.5
110J1339tight thermal0.010.5
111K1339tight thermal0.010.5
112L1339tight thermal0.010.5
21B1339tight thermal0.010.5
22A1339tight thermal0.010.5
23C1339tight thermal0.010.5
24D1339tight thermal0.010.5
25E1339tight thermal0.010.5
26F1339tight thermal0.010.5
27G1339tight thermal0.010.5
28H1339tight thermal0.010.5
29I1339tight thermal0.010.5
210J1339tight thermal0.010.5
211K1339tight thermal0.010.5
212L1339tight thermal0.010.5
31C1339tight thermal0.010.5
32A1339tight thermal0.010.5
33B1339tight thermal0.010.5
34D1339tight thermal0.010.5
35E1339tight thermal0.010.5
36F1339tight thermal0.010.5
37G1339tight thermal0.010.5
38H1339tight thermal0.010.5
39I1339tight thermal0.010.5
310J1339tight thermal0.010.5
311K1339tight thermal0.010.5
312L1339tight thermal0.010.5
41D1339tight thermal0.010.5
42A1339tight thermal0.010.5
43B1339tight thermal0.010.5
44C1339tight thermal0.010.5
45E1339tight thermal0.010.5
46F1339tight thermal0.010.5
47G1339tight thermal0.010.5
48H1339tight thermal0.010.5
49I1339tight thermal0.010.5
410J1339tight thermal0.010.5
411K1339tight thermal0.010.5
412L1339tight thermal0.010.5
51E1339tight thermal0.010.5
52A1339tight thermal0.010.5
53B1339tight thermal0.010.5
54C1339tight thermal0.010.5
55D1339tight thermal0.010.5
56F1339tight thermal0.010.5
57G1339tight thermal0.010.5
58H1339tight thermal0.010.5
59I1339tight thermal0.010.5
510J1339tight thermal0.010.5
511K1339tight thermal0.010.5
512L1339tight thermal0.010.5
61F1339tight thermal0.010.5
62A1339tight thermal0.010.5
63B1339tight thermal0.010.5
64C1339tight thermal0.010.5
65D1339tight thermal0.010.5
66E1339tight thermal0.010.5
67G1339tight thermal0.010.5
68H1339tight thermal0.010.5
69I1339tight thermal0.010.5
610J1339tight thermal0.010.5
611K1339tight thermal0.010.5
612L1339tight thermal0.010.5
71G1339tight thermal0.010.5
72A1339tight thermal0.010.5
73B1339tight thermal0.010.5
74C1339tight thermal0.010.5
75D1339tight thermal0.010.5
76E1339tight thermal0.010.5
77F1339tight thermal0.010.5
78H1339tight thermal0.010.5
79I1339tight thermal0.010.5
710J1339tight thermal0.010.5
711K1339tight thermal0.010.5
712L1339tight thermal0.010.5
81H1339tight thermal0.010.5
82A1339tight thermal0.010.5
83B1339tight thermal0.010.5
84C1339tight thermal0.010.5
85D1339tight thermal0.010.5
86E1339tight thermal0.010.5
87F1339tight thermal0.010.5
88G1339tight thermal0.010.5
89I1339tight thermal0.010.5
810J1339tight thermal0.010.5
811K1339tight thermal0.010.5
812L1339tight thermal0.010.5
91I1339tight thermal0.010.5
92A1339tight thermal0.010.5
93B1339tight thermal0.010.5
94C1339tight thermal0.010.5
95D1339tight thermal0.010.5
96E1339tight thermal0.010.5
97F1339tight thermal0.010.5
98G1339tight thermal0.010.5
99H1339tight thermal0.010.5
910J1339tight thermal0.010.5
911K1339tight thermal0.010.5
912L1339tight thermal0.010.5
101J1339tight thermal0.010.5
102A1339tight thermal0.010.5
103B1339tight thermal0.010.5
104C1339tight thermal0.010.5
105D1339tight thermal0.010.5
106E1339tight thermal0.010.5
107F1339tight thermal0.010.5
108G1339tight thermal0.010.5
109H1339tight thermal0.010.5
1010I1339tight thermal0.010.5
1011K1339tight thermal0.010.5
1012L1339tight thermal0.010.5
111K1339tight thermal0.010.5
112A1339tight thermal0.010.5
113B1339tight thermal0.010.5
114C1339tight thermal0.010.5
115D1339tight thermal0.010.5
116E1339tight thermal0.010.5
117F1339tight thermal0.010.5
118G1339tight thermal0.010.5
119H1339tight thermal0.010.5
1110I1339tight thermal0.010.5
1111J1339tight thermal0.010.5
1112L1339tight thermal0.010.5
121L1339tight thermal0.010.5
122A1339tight thermal0.010.5
123B1339tight thermal0.010.5
124C1339tight thermal0.010.5
125D1339tight thermal0.010.5
126E1339tight thermal0.010.5
127F1339tight thermal0.010.5
128G1339tight thermal0.010.5
129H1339tight thermal0.010.5
1210I1339tight thermal0.010.5
1211J1339tight thermal0.010.5
1212K1339tight thermal0.010.5
131B43tight thermal0.020.5
132D43tight thermal0.010.5
133F43tight thermal0.020.5
134H43tight thermal0.010.5
135J43tight thermal0.020.5
136L43tight thermal0.020.5
141D43tight thermal0.010.5
142B43tight thermal0.020.5
143F43tight thermal0.020.5
144H43tight thermal0.010.5
145J43tight thermal0.020.5
146L43tight thermal0.020.5
151F43tight thermal0.020.5
152B43tight thermal0.020.5
153D43tight thermal0.010.5
154H43tight thermal0.010.5
155J43tight thermal0.020.5
156L43tight thermal0.020.5
161H43tight thermal0.010.5
162B43tight thermal0.020.5
163D43tight thermal0.010.5
164F43tight thermal0.020.5
165J43tight thermal0.020.5
166L43tight thermal0.020.5
171J43tight thermal0.010.5
172B43tight thermal0.020.5
173D43tight thermal0.010.5
174F43tight thermal0.010.5
175H43tight thermal0.010.5
171J43tight thermal0.010.5
181L43tight thermal0.020.5
182B43tight thermal0.020.5
183D43tight thermal0.010.5
184F43tight thermal0.020.5
185H43tight thermal0.010.5
186J43tight thermal0.020.5
LS精密化 シェル解像度: 2.6→2.67 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.382 278 -
Rwork0.362 5198 -
obs--79.09 %

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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