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- PDB-5dzk: Crystal structure of the active form of the proteolytic complex c... -

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基本情報

登録情報
データベース: PDB / ID: 5dzk
タイトルCrystal structure of the active form of the proteolytic complex clpP1 and clpP2
要素
  • ATP-dependent Clp protease proteolytic subunit 1
  • ATP-dependent Clp protease proteolytic subunit 2
  • BEZ-LEU-LEU
キーワードHYDROLASE
機能・相同性
機能・相同性情報


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / peptidoglycan-based cell wall / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
類似検索 - ドメイン・相同性
Inhibitor BEZ-LEU-LEU / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1 / ATP-dependent Clp protease proteolytic subunit 1
類似検索 - 構成要素
生物種Mycobacterium tuberculosis (結核菌)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 解像度: 3.07 Å
データ登録者LI, M. / Wlodawer, A. / Maurizi, M.
引用ジャーナル: J.Biol.Chem. / : 2016
タイトル: Structure and Functional Properties of the Active Form of the Proteolytic Complex, ClpP1P2, from Mycobacterium tuberculosis.
著者: Li, M. / Kandror, O. / Akopian, T. / Dharkar, P. / Wlodawer, A. / Maurizi, M.R. / Goldberg, A.L.
履歴
登録2015年9月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年2月17日Provider: repository / タイプ: Initial release
改定 1.12016年2月24日Group: Database references
改定 1.22016年4月13日Group: Database references
改定 1.32025年4月2日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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集合体

登録構造単位
A: ATP-dependent Clp protease proteolytic subunit 2
O: BEZ-LEU-LEU
B: ATP-dependent Clp protease proteolytic subunit 2
P: BEZ-LEU-LEU
C: ATP-dependent Clp protease proteolytic subunit 2
Q: BEZ-LEU-LEU
D: ATP-dependent Clp protease proteolytic subunit 2
R: BEZ-LEU-LEU
E: ATP-dependent Clp protease proteolytic subunit 2
S: BEZ-LEU-LEU
F: ATP-dependent Clp protease proteolytic subunit 2
T: BEZ-LEU-LEU
G: ATP-dependent Clp protease proteolytic subunit 2
U: BEZ-LEU-LEU
H: ATP-dependent Clp protease proteolytic subunit 1
V: BEZ-LEU-LEU
I: ATP-dependent Clp protease proteolytic subunit 1
W: BEZ-LEU-LEU
J: ATP-dependent Clp protease proteolytic subunit 1
X: BEZ-LEU-LEU
K: ATP-dependent Clp protease proteolytic subunit 1
Y: BEZ-LEU-LEU
L: ATP-dependent Clp protease proteolytic subunit 1
Z: BEZ-LEU-LEU
M: ATP-dependent Clp protease proteolytic subunit 1
1: BEZ-LEU-LEU
N: ATP-dependent Clp protease proteolytic subunit 1
2: BEZ-LEU-LEU
a: ATP-dependent Clp protease proteolytic subunit 2
o: BEZ-LEU-LEU
b: ATP-dependent Clp protease proteolytic subunit 2
p: BEZ-LEU-LEU
c: ATP-dependent Clp protease proteolytic subunit 2
q: BEZ-LEU-LEU
d: ATP-dependent Clp protease proteolytic subunit 2
r: BEZ-LEU-LEU
e: ATP-dependent Clp protease proteolytic subunit 2
s: BEZ-LEU-LEU
f: ATP-dependent Clp protease proteolytic subunit 2
t: BEZ-LEU-LEU
g: ATP-dependent Clp protease proteolytic subunit 2
u: BEZ-LEU-LEU
h: ATP-dependent Clp protease proteolytic subunit 1
v: BEZ-LEU-LEU
i: ATP-dependent Clp protease proteolytic subunit 1
w: BEZ-LEU-LEU
j: ATP-dependent Clp protease proteolytic subunit 1
x: BEZ-LEU-LEU
k: ATP-dependent Clp protease proteolytic subunit 1
y: BEZ-LEU-LEU
l: ATP-dependent Clp protease proteolytic subunit 1
z: BEZ-LEU-LEU
m: ATP-dependent Clp protease proteolytic subunit 1
3: BEZ-LEU-LEU
n: ATP-dependent Clp protease proteolytic subunit 1
4: BEZ-LEU-LEU


分子量 (理論値)分子数
合計 (水以外)643,82256
ポリマ-643,82256
非ポリマー00
95553
1
A: ATP-dependent Clp protease proteolytic subunit 2
O: BEZ-LEU-LEU
B: ATP-dependent Clp protease proteolytic subunit 2
P: BEZ-LEU-LEU
C: ATP-dependent Clp protease proteolytic subunit 2
Q: BEZ-LEU-LEU
D: ATP-dependent Clp protease proteolytic subunit 2
R: BEZ-LEU-LEU
E: ATP-dependent Clp protease proteolytic subunit 2
S: BEZ-LEU-LEU
F: ATP-dependent Clp protease proteolytic subunit 2
T: BEZ-LEU-LEU
G: ATP-dependent Clp protease proteolytic subunit 2
U: BEZ-LEU-LEU
H: ATP-dependent Clp protease proteolytic subunit 1
V: BEZ-LEU-LEU
I: ATP-dependent Clp protease proteolytic subunit 1
W: BEZ-LEU-LEU
J: ATP-dependent Clp protease proteolytic subunit 1
X: BEZ-LEU-LEU
K: ATP-dependent Clp protease proteolytic subunit 1
Y: BEZ-LEU-LEU
L: ATP-dependent Clp protease proteolytic subunit 1
Z: BEZ-LEU-LEU
M: ATP-dependent Clp protease proteolytic subunit 1
1: BEZ-LEU-LEU
N: ATP-dependent Clp protease proteolytic subunit 1
2: BEZ-LEU-LEU


分子量 (理論値)分子数
合計 (水以外)321,91128
ポリマ-321,91128
非ポリマー00
21612
タイプ名称対称操作
identity operation1_555x,y,z1
2
a: ATP-dependent Clp protease proteolytic subunit 2
o: BEZ-LEU-LEU
b: ATP-dependent Clp protease proteolytic subunit 2
p: BEZ-LEU-LEU
c: ATP-dependent Clp protease proteolytic subunit 2
q: BEZ-LEU-LEU
d: ATP-dependent Clp protease proteolytic subunit 2
r: BEZ-LEU-LEU
e: ATP-dependent Clp protease proteolytic subunit 2
s: BEZ-LEU-LEU
f: ATP-dependent Clp protease proteolytic subunit 2
t: BEZ-LEU-LEU
g: ATP-dependent Clp protease proteolytic subunit 2
u: BEZ-LEU-LEU
h: ATP-dependent Clp protease proteolytic subunit 1
v: BEZ-LEU-LEU
i: ATP-dependent Clp protease proteolytic subunit 1
w: BEZ-LEU-LEU
j: ATP-dependent Clp protease proteolytic subunit 1
x: BEZ-LEU-LEU
k: ATP-dependent Clp protease proteolytic subunit 1
y: BEZ-LEU-LEU
l: ATP-dependent Clp protease proteolytic subunit 1
z: BEZ-LEU-LEU
m: ATP-dependent Clp protease proteolytic subunit 1
3: BEZ-LEU-LEU
n: ATP-dependent Clp protease proteolytic subunit 1
4: BEZ-LEU-LEU


分子量 (理論値)分子数
合計 (水以外)321,91128
ポリマ-321,91128
非ポリマー00
21612
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)205.940, 183.350, 188.450
Angle α, β, γ (deg.)90.00, 94.44, 90.00
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27a
18A
28b
19A
29c
110A
210d
111A
211e
112A
212f
113A
213g
114B
214C
115B
215D
116B
216E
117B
217F
118B
218G
119B
219a
120B
220b
121B
221c
122B
222d
123B
223e
124B
224f
125B
225g
126C
226D
127C
227E
128C
228F
129C
229G
130C
230a
131C
231b
132C
232c
133C
233d
134C
234e
135C
235f
136C
236g
137D
237E
138D
238F
139D
239G
140D
240a
141D
241b
142D
242c
143D
243d
144D
244e
145D
245f
146D
246g
147E
247F
148E
248G
149E
249a
150E
250b
151E
251c
152E
252d
153E
253e
154E
254f
155E
255g
156F
256G
157F
257a
158F
258b
159F
259c
160F
260d
161F
261e
162F
262f
163F
263g
164G
264a
165G
265b
166G
266c
167G
267d
168G
268e
169G
269f
170G
270g
171H
271I
172H
272J
173H
273K
174H
274L
175H
275M
176H
276N
177H
277h
178H
278i
179H
279j
180H
280k
181H
281l
182H
282m
183H
283n
184I
284J
185I
285K
186I
286L
187I
287M
188I
288N
189I
289h
190I
290i
191I
291j
192I
292k
193I
293l
194I
294m
195I
295n
196J
296K
197J
297L
198J
298M
199J
299N
1100J
2100h
1101J
2101i
1102J
2102j
1103J
2103k
1104J
2104l
1105J
2105m
1106J
2106n
1107K
2107L
1108K
2108M
1109K
2109N
1110K
2110h
1111K
2111i
1112K
2112j
1113K
2113k
1114K
2114l
1115K
2115m
1116K
2116n
1117L
2117M
1118L
2118N
1119L
2119h
1120L
2120i
1121L
2121j
1122L
2122k
1123L
2123l
1124L
2124m
1125L
2125n
1126M
2126N
1127M
2127h
1128M
2128i
1129M
2129j
1130M
2130k
1131M
2131l
1132M
2132m
1133M
2133n
1134N
2134h
1135N
2135i
1136N
2136j
1137N
2137k
1138N
2138l
1139N
2139m
1140N
2140n
1141a
2141b
1142a
2142c
1143a
2143d
1144a
2144e
1145a
2145f
1146a
2146g
1147b
2147c
1148b
2148d
1149b
2149e
1150b
2150f
1151b
2151g
1152c
2152d
1153c
2153e
1154c
2154f
1155c
2155g
1156d
2156e
1157d
2157f
1158d
2158g
1159e
2159f
1160e
2160g
1161f
2161g
1162h
2162i
1163h
2163j
1164h
2164k
1165h
2165l
1166h
2166m
1167h
2167n
1168i
2168j
1169i
2169k
1170i
2170l
1171i
2171m
1172i
2172n
1173j
2173k
1174j
2174l
1175j
2175m
1176j
2176n
1177k
2177l
1178k
2178m
1179k
2179n
1180l
2180m
1181l
2181n
1182m
2182n

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
11ILEILELEULEUAA15 - 20915 - 209
21ILEILELEULEUBC15 - 20915 - 209
12ILEILESERSERAA15 - 21015 - 210
22ILEILESERSERCE15 - 21015 - 210
13ILEILESERSERAA15 - 21015 - 210
23ILEILESERSERDG15 - 21015 - 210
14ILEILELEULEUAA15 - 20915 - 209
24ILEILELEULEUEI15 - 20915 - 209
15ILEILESERSERAA15 - 21015 - 210
25ILEILESERSERFK15 - 21015 - 210
16ILEILELYSLYSAA15 - 20815 - 208
26ILEILELYSLYSGM15 - 20815 - 208
17ILEILELEULEUAA15 - 20915 - 209
27ILEILELEULEUaCA15 - 20915 - 209
18ILEILELEULEUAA15 - 20915 - 209
28ILEILELEULEUbEA15 - 20915 - 209
19ILEILELEULEUAA15 - 20915 - 209
29ILEILELEULEUcGA15 - 20915 - 209
110ILEILESERSERAA15 - 21015 - 210
210ILEILESERSERdIA15 - 21015 - 210
111ILEILELEULEUAA15 - 20915 - 209
211ILEILELEULEUeKA15 - 20915 - 209
112ILEILESERSERAA15 - 21015 - 210
212ILEILESERSERfMA15 - 21015 - 210
113ILEILESERSERAA15 - 21015 - 210
213ILEILESERSERgOA15 - 21015 - 210
114ILEILELEULEUBC15 - 20915 - 209
214ILEILELEULEUCE15 - 20915 - 209
115ILEILELEULEUBC15 - 20915 - 209
215ILEILELEULEUDG15 - 20915 - 209
116ILEILEALAALABC15 - 21415 - 214
216ILEILEALAALAEI15 - 21415 - 214
117ILEILELEULEUBC15 - 20915 - 209
217ILEILELEULEUFK15 - 20915 - 209
118ILEILELYSLYSBC15 - 20815 - 208
218ILEILELYSLYSGM15 - 20815 - 208
119ILEILESERSERBC15 - 21015 - 210
219ILEILESERSERaCA15 - 21015 - 210
120ILEILEALAALABC15 - 21415 - 214
220ILEILEALAALAbEA15 - 21415 - 214
121ILEILESERSERBC15 - 21015 - 210
221ILEILESERSERcGA15 - 21015 - 210
122ILEILELEULEUBC15 - 20915 - 209
222ILEILELEULEUdIA15 - 20915 - 209
123ILEILEALAALABC15 - 21415 - 214
223ILEILEALAALAeKA15 - 21415 - 214
124ILEILELEULEUBC15 - 20915 - 209
224ILEILELEULEUfMA15 - 20915 - 209
125ILEILELEULEUBC15 - 20915 - 209
225ILEILELEULEUgOA15 - 20915 - 209
126ILEILESERSERCE15 - 21015 - 210
226ILEILESERSERDG15 - 21015 - 210
127ILEILELEULEUCE15 - 20915 - 209
227ILEILELEULEUEI15 - 20915 - 209
128ILEILESERSERCE15 - 21015 - 210
228ILEILESERSERFK15 - 21015 - 210
129ILEILELYSLYSCE15 - 20815 - 208
229ILEILELYSLYSGM15 - 20815 - 208
130ILEILELEULEUCE15 - 20915 - 209
230ILEILELEULEUaCA15 - 20915 - 209
131ILEILELEULEUCE15 - 20915 - 209
231ILEILELEULEUbEA15 - 20915 - 209
132ILEILELEULEUCE15 - 20915 - 209
232ILEILELEULEUcGA15 - 20915 - 209
133ILEILESERSERCE15 - 21015 - 210
233ILEILESERSERdIA15 - 21015 - 210
134ILEILELEULEUCE15 - 20915 - 209
234ILEILELEULEUeKA15 - 20915 - 209
135ILEILESERSERCE15 - 21015 - 210
235ILEILESERSERfMA15 - 21015 - 210
136ILEILESERSERCE15 - 21015 - 210
236ILEILESERSERgOA15 - 21015 - 210
137ILEILELEULEUDG15 - 20915 - 209
237ILEILELEULEUEI15 - 20915 - 209
138ILEILESERSERDG15 - 21015 - 210
238ILEILESERSERFK15 - 21015 - 210
139ILEILELYSLYSDG15 - 20815 - 208
239ILEILELYSLYSGM15 - 20815 - 208
140ILEILELEULEUDG15 - 20915 - 209
240ILEILELEULEUaCA15 - 20915 - 209
141ILEILELEULEUDG15 - 20915 - 209
241ILEILELEULEUbEA15 - 20915 - 209
142ILEILELEULEUDG15 - 20915 - 209
242ILEILELEULEUcGA15 - 20915 - 209
143ILEILESERSERDG15 - 21015 - 210
243ILEILESERSERdIA15 - 21015 - 210
144ILEILELEULEUDG15 - 20915 - 209
244ILEILELEULEUeKA15 - 20915 - 209
145ILEILESERSERDG15 - 21015 - 210
245ILEILESERSERfMA15 - 21015 - 210
146ILEILESERSERDG15 - 21015 - 210
246ILEILESERSERgOA15 - 21015 - 210
147ILEILELEULEUEI15 - 20915 - 209
247ILEILELEULEUFK15 - 20915 - 209
148ILEILELYSLYSEI15 - 20815 - 208
248ILEILELYSLYSGM15 - 20815 - 208
149ILEILESERSEREI15 - 21015 - 210
249ILEILESERSERaCA15 - 21015 - 210
150ILEILEALAALAEI15 - 21415 - 214
250ILEILEALAALAbEA15 - 21415 - 214
151ILEILESERSEREI15 - 21015 - 210
251ILEILESERSERcGA15 - 21015 - 210
152ILEILELEULEUEI15 - 20915 - 209
252ILEILELEULEUdIA15 - 20915 - 209
153ILEILEALAALAEI15 - 21415 - 214
253ILEILEALAALAeKA15 - 21415 - 214
154ILEILELEULEUEI15 - 20915 - 209
254ILEILELEULEUfMA15 - 20915 - 209
155ILEILELEULEUEI15 - 20915 - 209
255ILEILELEULEUgOA15 - 20915 - 209
156ILEILELYSLYSFK15 - 20815 - 208
256ILEILELYSLYSGM15 - 20815 - 208
157ILEILELEULEUFK15 - 20915 - 209
257ILEILELEULEUaCA15 - 20915 - 209
158ILEILELEULEUFK15 - 20915 - 209
258ILEILELEULEUbEA15 - 20915 - 209
159ILEILELEULEUFK15 - 20915 - 209
259ILEILELEULEUcGA15 - 20915 - 209
160ILEILESERSERFK15 - 21015 - 210
260ILEILESERSERdIA15 - 21015 - 210
161ILEILELEULEUFK15 - 20915 - 209
261ILEILELEULEUeKA15 - 20915 - 209
162ILEILESERSERFK15 - 21015 - 210
262ILEILESERSERfMA15 - 21015 - 210
163ILEILESERSERFK15 - 21015 - 210
263ILEILESERSERgOA15 - 21015 - 210
164ILEILELYSLYSGM15 - 20815 - 208
264ILEILELYSLYSaCA15 - 20815 - 208
165ILEILELYSLYSGM15 - 20815 - 208
265ILEILELYSLYSbEA15 - 20815 - 208
166ILEILELYSLYSGM15 - 20815 - 208
266ILEILELYSLYScGA15 - 20815 - 208
167ILEILELYSLYSGM15 - 20815 - 208
267ILEILELYSLYSdIA15 - 20815 - 208
168ILEILELYSLYSGM15 - 20815 - 208
268ILEILELYSLYSeKA15 - 20815 - 208
169ILEILELYSLYSGM15 - 20815 - 208
269ILEILELYSLYSfMA15 - 20815 - 208
170ILEILELYSLYSGM15 - 20815 - 208
270ILEILELYSLYSgOA15 - 20815 - 208
171SERSERARGARGHO15 - 19215 - 192
271SERSERARGARGIQ15 - 19215 - 192
172SERSERARGARGHO15 - 19215 - 192
272SERSERARGARGJS15 - 19215 - 192
173SERSERARGARGHO15 - 19215 - 192
273SERSERARGARGKU15 - 19215 - 192
174SERSERARGARGHO15 - 19215 - 192
274SERSERARGARGLW15 - 19215 - 192
175SERSERARGARGHO15 - 19215 - 192
275SERSERARGARGMY15 - 19215 - 192
176SERSERTHRTHRHO15 - 19115 - 191
276SERSERTHRTHRNAA15 - 19115 - 191
177SERSERARGARGHO15 - 19215 - 192
277SERSERARGARGhQA15 - 19215 - 192
178SERSERARGARGHO15 - 19215 - 192
278SERSERARGARGiSA15 - 19215 - 192
179SERSERARGARGHO15 - 19215 - 192
279SERSERARGARGjUA15 - 19215 - 192
180SERSERARGARGHO15 - 19215 - 192
280SERSERARGARGkWA15 - 19215 - 192
181SERSERARGARGHO15 - 19215 - 192
281SERSERARGARGlYA15 - 19215 - 192
182SERSERARGARGHO15 - 19215 - 192
282SERSERARGARGmAB15 - 19215 - 192
183SERSERARGARGHO15 - 19215 - 192
283SERSERARGARGnCB15 - 19215 - 192
184SERSERARGARGIQ15 - 19215 - 192
284SERSERARGARGJS15 - 19215 - 192
185SERSERARGARGIQ15 - 19215 - 192
285SERSERARGARGKU15 - 19215 - 192
186SERSERARGARGIQ15 - 19215 - 192
286SERSERARGARGLW15 - 19215 - 192
187SERSERARGARGIQ15 - 19215 - 192
287SERSERARGARGMY15 - 19215 - 192
188SERSERTHRTHRIQ15 - 19115 - 191
288SERSERTHRTHRNAA15 - 19115 - 191
189SERSERARGARGIQ15 - 19215 - 192
289SERSERARGARGhQA15 - 19215 - 192
190SERSERARGARGIQ15 - 19215 - 192
290SERSERARGARGiSA15 - 19215 - 192
191SERSERARGARGIQ15 - 19215 - 192
291SERSERARGARGjUA15 - 19215 - 192
192SERSERARGARGIQ15 - 19215 - 192
292SERSERARGARGkWA15 - 19215 - 192
193SERSERARGARGIQ15 - 19215 - 192
293SERSERARGARGlYA15 - 19215 - 192
194SERSERARGARGIQ15 - 19215 - 192
294SERSERARGARGmAB15 - 19215 - 192
195SERSERARGARGIQ15 - 19215 - 192
295SERSERARGARGnCB15 - 19215 - 192
196SERSERARGARGJS15 - 19215 - 192
296SERSERARGARGKU15 - 19215 - 192
197SERSERARGARGJS15 - 19215 - 192
297SERSERARGARGLW15 - 19215 - 192
198SERSERARGARGJS15 - 19215 - 192
298SERSERARGARGMY15 - 19215 - 192
199SERSERTHRTHRJS15 - 19115 - 191
299SERSERTHRTHRNAA15 - 19115 - 191
1100SERSERARGARGJS15 - 19215 - 192
2100SERSERARGARGhQA15 - 19215 - 192
1101SERSERARGARGJS15 - 19215 - 192
2101SERSERARGARGiSA15 - 19215 - 192
1102SERSERARGARGJS15 - 19215 - 192
2102SERSERARGARGjUA15 - 19215 - 192
1103SERSERARGARGJS15 - 19215 - 192
2103SERSERARGARGkWA15 - 19215 - 192
1104SERSERARGARGJS15 - 19215 - 192
2104SERSERARGARGlYA15 - 19215 - 192
1105SERSERARGARGJS15 - 19215 - 192
2105SERSERARGARGmAB15 - 19215 - 192
1106SERSERARGARGJS15 - 19215 - 192
2106SERSERARGARGnCB15 - 19215 - 192
1107SERSERARGARGKU15 - 19215 - 192
2107SERSERARGARGLW15 - 19215 - 192
1108SERSERARGARGKU15 - 19215 - 192
2108SERSERARGARGMY15 - 19215 - 192
1109SERSERTHRTHRKU15 - 19115 - 191
2109SERSERTHRTHRNAA15 - 19115 - 191
1110SERSERARGARGKU15 - 19215 - 192
2110SERSERARGARGhQA15 - 19215 - 192
1111SERSERARGARGKU15 - 19215 - 192
2111SERSERARGARGiSA15 - 19215 - 192
1112SERSERARGARGKU15 - 19215 - 192
2112SERSERARGARGjUA15 - 19215 - 192
1113SERSERARGARGKU15 - 19215 - 192
2113SERSERARGARGkWA15 - 19215 - 192
1114SERSERARGARGKU15 - 19215 - 192
2114SERSERARGARGlYA15 - 19215 - 192
1115SERSERARGARGKU15 - 19215 - 192
2115SERSERARGARGmAB15 - 19215 - 192
1116SERSERARGARGKU15 - 19215 - 192
2116SERSERARGARGnCB15 - 19215 - 192
1117SERSERARGARGLW15 - 19215 - 192
2117SERSERARGARGMY15 - 19215 - 192
1118SERSERTHRTHRLW15 - 19115 - 191
2118SERSERTHRTHRNAA15 - 19115 - 191
1119SERSERARGARGLW15 - 19215 - 192
2119SERSERARGARGhQA15 - 19215 - 192
1120SERSERARGARGLW15 - 19215 - 192
2120SERSERARGARGiSA15 - 19215 - 192
1121SERSERARGARGLW15 - 19215 - 192
2121SERSERARGARGjUA15 - 19215 - 192
1122SERSERARGARGLW15 - 19215 - 192
2122SERSERARGARGkWA15 - 19215 - 192
1123SERSERARGARGLW15 - 19215 - 192
2123SERSERARGARGlYA15 - 19215 - 192
1124SERSERARGARGLW15 - 19215 - 192
2124SERSERARGARGmAB15 - 19215 - 192
1125SERSERARGARGLW15 - 19215 - 192
2125SERSERARGARGnCB15 - 19215 - 192
1126SERSERTHRTHRMY15 - 19115 - 191
2126SERSERTHRTHRNAA15 - 19115 - 191
1127SERSERARGARGMY15 - 19215 - 192
2127SERSERARGARGhQA15 - 19215 - 192
1128SERSERARGARGMY15 - 19215 - 192
2128SERSERARGARGiSA15 - 19215 - 192
1129SERSERARGARGMY15 - 19215 - 192
2129SERSERARGARGjUA15 - 19215 - 192
1130SERSERARGARGMY15 - 19215 - 192
2130SERSERARGARGkWA15 - 19215 - 192
1131SERSERARGARGMY15 - 19215 - 192
2131SERSERARGARGlYA15 - 19215 - 192
1132SERSERARGARGMY15 - 19215 - 192
2132SERSERARGARGmAB15 - 19215 - 192
1133SERSERARGARGMY15 - 19215 - 192
2133SERSERARGARGnCB15 - 19215 - 192
1134SERSERTHRTHRNAA15 - 19115 - 191
2134SERSERTHRTHRhQA15 - 19115 - 191
1135SERSERTHRTHRNAA15 - 19115 - 191
2135SERSERTHRTHRiSA15 - 19115 - 191
1136SERSERTHRTHRNAA15 - 19115 - 191
2136SERSERTHRTHRjUA15 - 19115 - 191
1137SERSERTHRTHRNAA15 - 19115 - 191
2137SERSERTHRTHRkWA15 - 19115 - 191
1138SERSERTHRTHRNAA15 - 19115 - 191
2138SERSERTHRTHRlYA15 - 19115 - 191
1139SERSERTHRTHRNAA15 - 19115 - 191
2139SERSERTHRTHRmAB15 - 19115 - 191
1140SERSERTHRTHRNAA15 - 19115 - 191
2140SERSERTHRTHRnCB15 - 19115 - 191
1141ILEILESERSERaCA15 - 21015 - 210
2141ILEILESERSERbEA15 - 21015 - 210
1142ILEILEALAALAaCA15 - 21115 - 211
2142ILEILEALAALAcGA15 - 21115 - 211
1143ILEILELEULEUaCA15 - 20915 - 209
2143ILEILELEULEUdIA15 - 20915 - 209
1144ILEILESERSERaCA15 - 21015 - 210
2144ILEILESERSEReKA15 - 21015 - 210
1145ILEILELEULEUaCA15 - 20915 - 209
2145ILEILELEULEUfMA15 - 20915 - 209
1146ILEILELEULEUaCA15 - 20915 - 209
2146ILEILELEULEUgOA15 - 20915 - 209
1147ILEILESERSERbEA15 - 21015 - 210
2147ILEILESERSERcGA15 - 21015 - 210
1148ILEILELEULEUbEA15 - 20915 - 209
2148ILEILELEULEUdIA15 - 20915 - 209
1149ILEILEALAALAbEA15 - 21415 - 214
2149ILEILEALAALAeKA15 - 21415 - 214
1150ILEILELEULEUbEA15 - 20915 - 209
2150ILEILELEULEUfMA15 - 20915 - 209
1151ILEILELEULEUbEA15 - 20915 - 209
2151ILEILELEULEUgOA15 - 20915 - 209
1152ILEILELEULEUcGA15 - 20915 - 209
2152ILEILELEULEUdIA15 - 20915 - 209
1153ILEILESERSERcGA15 - 21015 - 210
2153ILEILESERSEReKA15 - 21015 - 210
1154ILEILELEULEUcGA15 - 20915 - 209
2154ILEILELEULEUfMA15 - 20915 - 209
1155ILEILELEULEUcGA15 - 20915 - 209
2155ILEILELEULEUgOA15 - 20915 - 209
1156ILEILELEULEUdIA15 - 20915 - 209
2156ILEILELEULEUeKA15 - 20915 - 209
1157ILEILESERSERdIA15 - 21015 - 210
2157ILEILESERSERfMA15 - 21015 - 210
1158ILEILESERSERdIA15 - 21015 - 210
2158ILEILESERSERgOA15 - 21015 - 210
1159ILEILELEULEUeKA15 - 20915 - 209
2159ILEILELEULEUfMA15 - 20915 - 209
1160ILEILELEULEUeKA15 - 20915 - 209
2160ILEILELEULEUgOA15 - 20915 - 209
1161ILEILESERSERfMA15 - 21015 - 210
2161ILEILESERSERgOA15 - 21015 - 210
1162SERSERARGARGhQA15 - 19215 - 192
2162SERSERARGARGiSA15 - 19215 - 192
1163SERSERARGARGhQA15 - 19215 - 192
2163SERSERARGARGjUA15 - 19215 - 192
1164SERSERARGARGhQA15 - 19215 - 192
2164SERSERARGARGkWA15 - 19215 - 192
1165SERSERARGARGhQA15 - 19215 - 192
2165SERSERARGARGlYA15 - 19215 - 192
1166SERSERARGARGhQA15 - 19215 - 192
2166SERSERARGARGmAB15 - 19215 - 192
1167SERSERARGARGhQA15 - 19215 - 192
2167SERSERARGARGnCB15 - 19215 - 192
1168SERSERARGARGiSA15 - 19215 - 192
2168SERSERARGARGjUA15 - 19215 - 192
1169SERSERARGARGiSA15 - 19215 - 192
2169SERSERARGARGkWA15 - 19215 - 192
1170SERSERARGARGiSA15 - 19215 - 192
2170SERSERARGARGlYA15 - 19215 - 192
1171SERSERARGARGiSA15 - 19215 - 192
2171SERSERARGARGmAB15 - 19215 - 192
1172SERSERARGARGiSA15 - 19215 - 192
2172SERSERARGARGnCB15 - 19215 - 192
1173SERSERARGARGjUA15 - 19215 - 192
2173SERSERARGARGkWA15 - 19215 - 192
1174SERSERARGARGjUA15 - 19215 - 192
2174SERSERARGARGlYA15 - 19215 - 192
1175SERSERARGARGjUA15 - 19215 - 192
2175SERSERARGARGmAB15 - 19215 - 192
1176SERSERARGARGjUA15 - 19215 - 192
2176SERSERARGARGnCB15 - 19215 - 192
1177SERSERARGARGkWA15 - 19215 - 192
2177SERSERARGARGlYA15 - 19215 - 192
1178SERSERARGARGkWA15 - 19215 - 192
2178SERSERARGARGmAB15 - 19215 - 192
1179SERSERARGARGkWA15 - 19215 - 192
2179SERSERARGARGnCB15 - 19215 - 192
1180SERSERARGARGlYA15 - 19215 - 192
2180SERSERARGARGmAB15 - 19215 - 192
1181SERSERARGARGlYA15 - 19215 - 192
2181SERSERARGARGnCB15 - 19215 - 192
1182SERSERARGARGmAB15 - 19215 - 192
2182SERSERARGARGnCB15 - 19215 - 192

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
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182

-
要素

#1: タンパク質
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


分子量: 23562.754 Da / 分子数: 14 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (結核菌)
: CDC 1551 / Oshkosh / 遺伝子: clpP2, MT2535 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P9WPC2, UniProt: P9WPC3*PLUS, endopeptidase Clp
#2: タンパク質・ペプチド ...
BEZ-LEU-LEU


タイプ: Peptide-like / クラス: 酵素阻害剤 / 分子量: 348.437 Da / 分子数: 28 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) / 参照: Inhibitor BEZ-LEU-LEU
#3: タンパク質
ATP-dependent Clp protease proteolytic subunit 1 / Endopeptidase Clp 1


分子量: 21727.664 Da / 分子数: 14 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (結核菌)
: CDC 1551 / Oshkosh / 遺伝子: clpP1, clpP, MT2536 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P9WPC4, UniProt: P9WPC5*PLUS, endopeptidase Clp
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 53 / 由来タイプ: 天然 / : H2O
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折

-
試料調製

結晶マシュー密度: 2.75 Å3/Da / 溶媒含有率: 55.35 %
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: 6.5 / 詳細: 25% PEG 3350

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2014年6月6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 Å / 相対比: 1
反射解像度: 3.07→100 Å / Num. obs: 129368 / % possible obs: 99.5 % / 冗長度: 4.22 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.33
反射 シェル解像度: 3.07→3.15 Å / 冗長度: 4.29 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.29

-
解析

ソフトウェア
名称バージョン分類
REFMAC5.7.0029精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化解像度: 3.07→72.24 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 44.69 / SU ML: 0.338 / 交差検証法: THROUGHOUT / ESU R Free: 0.442 / 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
Rfree0.23167 6092 5 %RANDOM
Rwork0.19822 ---
obs0.19989 115022 93.18 %-
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: 67.125 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å2-0 Å2-1.35 Å2
2---2.54 Å2-0 Å2
3---6.1 Å2
精密化ステップサイクル: LAST / 解像度: 3.07→72.24 Å
タンパク質核酸リガンド溶媒全体
原子数40923 0 0 53 40976
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01941525
X-RAY DIFFRACTIONr_bond_other_d0.0090.0240413
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.98356129
X-RAY DIFFRACTIONr_angle_other_deg2.056392779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27755254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01224.1861782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.749157249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.33215294
X-RAY DIFFRACTIONr_chiral_restr0.0910.26518
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0246938
X-RAY DIFFRACTIONr_gen_planes_other0.0070.029056
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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-IDRms dev position (Å)
11A116420.07
12B116420.07
21A114790.08
22C114790.08
31A115240.09
32D115240.09
41A116190.07
42E116190.07
51A114540.09
52F114540.09
61A115380.07
62G115380.07
71A116530.07
72a116530.07
81A115630.07
82b115630.07
91A114630.09
92c114630.09
101A115080.08
102d115080.08
111A114520.09
112e114520.09
121A116630.07
122f116630.07
131A116240.07
132g116240.07
141B114320.09
142C114320.09
151B115110.09
152D115110.09
161B116810.08
162E116810.08
171B114250.08
172F114250.08
181B115100.07
182G115100.07
191B115740.07
192a115740.07
201B115480.09
202b115480.09
211B115990.07
212c115990.07
221B115450.08
222d115450.08
231B116270.08
232e116270.08
241B115480.08
242f115480.08
251B116090.07
252g116090.07
261C115090.09
262D115090.09
271C115900.08
272E115900.08
281C113970.09
282F113970.09
291C115010.08
292G115010.08
301C114660.08
302a114660.08
311C114080.08
312b114080.08
321C114780.08
322c114780.08
331C114830.08
332d114830.08
341C113680.09
342e113680.09
351C116020.08
352f116020.08
361C115570.08
362g115570.08
371D116490.08
372E116490.08
381D114980.1
382F114980.1
391D114850.08
392G114850.08
401D115060.08
402a115060.08
411D114520.09
412b114520.09
421D114970.09
422c114970.09
431D116520.09
432d116520.09
441D115780.09
442e115780.09
451D116170.09
452f116170.09
461D115920.09
462g115920.09
471E114230.09
472F114230.09
481E116980.06
482G116980.06
491E118220.05
492a118220.05
501E116690.08
502b116690.08
511E117080.07
512c117080.07
521E115760.08
522d115760.08
531E118250.07
532e118250.07
541E117400.07
542f117400.07
551E117420.07
552g117420.07
561F113640.09
562G113640.09
571F113640.09
572a113640.09
581F113620.09
582b113620.09
591F114620.09
592c114620.09
601F115680.08
602d115680.08
611F114990.09
612e114990.09
621F115640.08
622f115640.08
631F114870.09
632g114870.09
641G115850.06
642a115850.06
651G114820.08
652b114820.08
661G115450.08
662c115450.08
671G114290.08
672d114290.08
681G115150.08
682e115150.08
691G116540.07
692f116540.07
701G116120.07
702g116120.07
711H104080.08
712I104080.08
721H105050.07
722J105050.07
731H103430.09
732K103430.09
741H103350.09
742L103350.09
751H103330.09
752M103330.09
761H102500.09
762N102500.09
771H104340.08
772h104340.08
781H104580.09
782i104580.09
791H103700.08
792j103700.08
801H103790.09
802k103790.09
811H104720.08
812l104720.08
821H104570.09
822m104570.09
831H103190.09
832n103190.09
841I104160.08
842J104160.08
851I102240.09
852K102240.09
861I102590.1
862L102590.1
871I103940.09
872M103940.09
881I102590.08
882N102590.08
891I102630.09
892h102630.09
901I104280.09
902i104280.09
911I104490.08
912j104490.08
921I102420.1
922k102420.1
931I104340.08
932l104340.08
941I103370.09
942m103370.09
951I103140.09
952n103140.09
961J102800.08
962K102800.08
971J103880.08
972L103880.08
981J103860.09
982M103860.09
991J102370.08
992N102370.08
1001J104080.07
1002h104080.07
1011J105190.07
1012i105190.07
1021J103950.08
1022j103950.08
1031J103480.08
1032k103480.08
1041J105210.07
1042l105210.07
1051J104630.07
1052m104630.07
1061J103540.07
1062n103540.07
1071K104030.09
1072L104030.09
1081K101640.1
1082M101640.1
1091K101700.09
1092N101700.09
1101K104790.08
1102h104790.08
1111K102690.09
1112i102690.09
1121K101870.09
1122j101870.09
1131K104030.09
1132k104030.09
1141K103260.08
1142l103260.08
1151K102850.09
1152m102850.09
1161K103700.08
1162n103700.08
1171L102930.09
1172M102930.09
1181L101690.09
1182N101690.09
1191L104230.09
1192h104230.09
1201L104050.08
1202i104050.08
1211L102410.09
1212j102410.09
1221L104630.07
1222k104630.07
1231L103490.09
1232l103490.09
1241L103230.09
1242m103230.09
1251L104670.08
1252n104670.08
1261M102510.09
1262N102510.09
1271M102570.09
1272h102570.09
1281M103770.09
1282i103770.09
1291M103020.09
1292j103020.09
1301M101880.11
1302k101880.11
1311M104320.08
1312l104320.08
1321M104350.08
1322m104350.08
1331M103560.09
1332n103560.09
1341N102080.09
1342h102080.09
1351N102320.09
1352i102320.09
1361N102780.08
1362j102780.08
1371N102530.09
1372k102530.09
1381N102180.09
1382l102180.09
1391N103400.08
1392m103400.08
1401N101770.09
1402n101770.09
1411a115930.07
1412b115930.07
1421a115720.08
1422c115720.08
1431a114860.08
1432d114860.08
1441a115630.07
1442e115630.07
1451a116850.06
1452f116850.06
1461a116360.07
1462g116360.07
1471b114570.09
1472c114570.09
1481b115350.08
1482d115350.08
1491b116330.09
1492e116330.09
1501b115720.08
1502f115720.08
1511b116250.08
1512g116250.08
1521c114700.08
1522d114700.08
1531c116430.07
1532e116430.07
1541c115720.09
1542f115720.09
1551c116310.07
1552g116310.07
1561d115880.08
1562e115880.08
1571d115560.08
1572f115560.08
1581d115660.08
1582g115660.08
1591e115270.08
1592f115270.08
1601e116520.06
1602g116520.06
1611f117340.07
1612g117340.07
1621h103660.09
1622i103660.09
1631h102220.09
1632j102220.09
1641h105160.08
1642k105160.08
1651h103850.08
1652l103850.08
1661h103760.08
1662m103760.08
1671h103860.08
1672n103860.08
1681i103210.09
1682j103210.09
1691i102350.1
1692k102350.1
1701i104060.08
1702l104060.08
1711i104380.08
1712m104380.08
1721i103770.08
1722n103770.08
1731j102520.09
1732k102520.09
1741j104420.07
1742l104420.07
1751j103000.08
1752m103000.08
1761j103350.08
1762n103350.08
1771k103720.08
1772l103720.08
1781k102750.1
1782m102750.1
1791k103750.09
1792n103750.09
1801l103800.08
1802m103800.08
1811l103900.09
1812n103900.09
1821m102690.09
1822n102690.09
LS精密化 シェル解像度: 3.07→3.15 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.341 384 -
Rwork0.313 7464 -
obs--81.96 %
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.55960.2561-0.46741.3128-0.23990.8881-0.0742-0.08370.0721-0.00630.19730.2138-0.0691-0.0741-0.12310.5480.0704-0.01770.5701-0.06910.69120.1481122.7143105.4441
21.157-0.2403-0.42260.5180.17730.7661-0.0753-0.10090.1674-0.07360.10020.12130.0052-0.1755-0.02490.564-0.026-0.0810.51170.01390.704324.688116.293480.7695
31.7134-0.6857-0.02111.29840.42260.6946-0.02410.0048-0.0522-0.22020.030.2887-0.001-0.1057-0.00590.5948-0.0555-0.09460.56390.07040.482827.133191.821670.1256
41.0682-0.71670.14161.1501-0.39790.6176-0.102-0.0413-0.1129-0.03780.08850.29790.1203-0.18590.01350.5725-0.075-0.03520.56130.04940.588824.833968.632782.2048
50.87090.21610.34430.46880.27791.2857-0.1684-0.1953-0.02160.25580.13250.3003-0.0408-0.11070.03590.55250.05170.0870.54820.11030.563219.869163.545107.1392
60.91820.0450.08361.01920.4371.1863-0.1082-0.1528-0.0590.32910.15220.23870.1205-0.0957-0.04390.64270.14910.11440.68240.06420.451716.267580.9223127.136
71.26410.24430.28331.61050.26630.458-0.0609-0.29710.05350.15560.07560.2522-0.0478-0.0994-0.01470.56640.14550.0870.7178-0.0510.424316.3735107.2738126.1368
80.3771-0.3497-0.28751.19240.12120.6216-0.0167-0.05270.2159-0.14710.1573-0.2503-0.14010.1484-0.14060.535-0.07390.03120.5795-0.16220.667170.5371118.21190.0033
90.9196-0.61430.45681.321-0.38871.15240.0025-0.05410.2381-0.20120.0083-0.2554-0.0030.126-0.01080.5823-0.0190.06240.596-0.09340.502672.928893.974477.8232
100.259-0.22080.0730.3538-0.31591.1581-0.1049-0.068-0.0556-0.07160.0836-0.05050.01480.27260.02130.64850.0750.01670.679-0.04250.48470.968369.057388.6892
110.88780.21190.35870.8125-0.0711.169-0.0438-0.1835-0.14590.13450.1925-0.09740.14240.1375-0.14870.64580.2245-0.0330.6340.00070.378566.068162.3312114.7028
122.1570.60620.36041.62740.21610.3907-0.1479-0.4766-0.01820.20510.1639-0.12490.05080.033-0.0160.73890.2377-0.0920.8284-0.01250.160762.101978.7935135.8622
130.77830.5012-0.40651.422-0.46680.8162-0.0777-0.30140.08830.37060.0761-0.102-0.03650.20350.00160.71310.1485-0.15280.8514-0.23290.227661.8852106.0385136.6231
141.47890.361-0.04190.9474-0.45770.39240.0172-0.15230.35670.15260.0386-0.1493-0.0650.1099-0.05580.5810.0205-0.1150.5813-0.28180.520265.719123.6257116.1905
150.67240.0882-0.36590.7389-0.38460.5617-0.17720.1159-0.1079-0.14150.15240.0577-0.0387-0.06690.02480.81590.0484-0.01010.681-0.01360.434127.4328120.079411.5278
160.7284-0.3022-0.56250.33580.12010.9905-0.13120.1554-0.1756-0.20320.10550.19880.0116-0.13850.02570.8312-0.0381-0.03330.63910.03820.476732.3154113.6142-13.1551
170.3387-0.63260.04151.52080.21020.2843-0.03120.01290.0387-0.0862-0.0029-0.0335-0.0020.03810.03410.5033-0.0502-0.0190.439-0.03110.011734.677689.1344-23.5558
180.0279-0.14350.06611.0641-0.3220.2712-0.02170.0285-0.0335-0.05920.08940.11130.05540.0682-0.06770.47680.0027-0.02450.3901-0.07790.125532.059465.92-11.4479
190.0543-0.07540.22430.4904-0.12491.02090.0071-0.005-0.03770.02590.14310.02630.05570.0241-0.15020.4213-0.00280.00950.3471-0.00930.205426.692360.875113.4231
200.2240.45850.38360.9860.72060.8453-0.0076-0.0333-0.01630.04920.0031-0.0370.0509-0.10570.00450.4130.02740.07050.41780.03020.071922.886578.323733.3618
210.39180.6946-0.08491.2825-0.1880.0771-0.0358-0.02530.01040.08020.00850.0292-0.1024-0.00640.02730.45990.06420.04510.4354-0.03680.053823.2135104.661932.208
220.5246-0.2883-0.23661.0691-0.13370.2231-0.0946-0.01710.0581-0.07270.1163-0.1152-0.0590.0101-0.02170.5013-0.10640.06010.3835-0.050.023578.047115.1777-3.241
230.3219-0.3267-0.11440.5114-0.22410.7858-0.00860.08350.0483-0.0533-0.0566-0.1223-0.03390.06570.06520.442-0.0230.08450.4899-0.10570.069580.433490.8452-15.0983
240.348-0.6760.02831.38340.12590.80820.0210.05890.0205-0.04260.0129-0.08790.11910.1145-0.03390.42280.02960.04940.4117-0.13540.057378.047665.9928-4.2047
250.10260.0014-0.16870.7183-0.11790.34330.00520.0201-0.02450.0916-0.0067-0.05980.0890.05950.00150.49860.0943-0.04390.3104-0.09010.134872.714859.355821.6381
260.1152-0.06660.10120.34580.10510.82690.0314-0.0136-0.06080.11060.0354-0.06010.0733-0.0455-0.06680.48980.0605-0.03970.3238-0.05270.072868.533475.898142.7282
270.07680.1939-0.1450.7186-0.16970.61470.075-0.0042-0.02690.0836-0.0854-0.0544-0.2110.02010.01030.49980.0093-0.01910.3557-0.07040.032968.4718103.115343.3488
281.6868-0.0075-0.2440.80340.11960.2058-0.1094-0.09520.0168-0.04840.158-0.1068-0.10440.0356-0.04860.5122-0.0443-0.0010.326-0.05420.026272.6723120.658622.9086
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 210
2X-RAY DIFFRACTION2B15 - 214
3X-RAY DIFFRACTION3C15 - 210
4X-RAY DIFFRACTION4D15 - 210
5X-RAY DIFFRACTION5E15 - 214
6X-RAY DIFFRACTION6F15 - 210
7X-RAY DIFFRACTION7G15 - 209
8X-RAY DIFFRACTION8H15 - 192
9X-RAY DIFFRACTION9I15 - 192
10X-RAY DIFFRACTION10J15 - 192
11X-RAY DIFFRACTION11K15 - 192
12X-RAY DIFFRACTION12L15 - 192
13X-RAY DIFFRACTION13M15 - 192
14X-RAY DIFFRACTION14N15 - 193
15X-RAY DIFFRACTION15a15 - 211
16X-RAY DIFFRACTION16b15 - 214
17X-RAY DIFFRACTION17c15 - 211
18X-RAY DIFFRACTION18d15 - 210
19X-RAY DIFFRACTION19e15 - 214
20X-RAY DIFFRACTION20f15 - 210
21X-RAY DIFFRACTION21g15 - 210
22X-RAY DIFFRACTION22h15 - 192
23X-RAY DIFFRACTION23i15 - 192
24X-RAY DIFFRACTION24j15 - 192
25X-RAY DIFFRACTION25k15 - 192
26X-RAY DIFFRACTION26l15 - 192
27X-RAY DIFFRACTION27m15 - 192
28X-RAY DIFFRACTION28n15 - 192

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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://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

+
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。

-
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