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- PDB-4b0j: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd... -

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基本情報

登録情報
データベース: PDB / ID: 4b0j
タイトルCrystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa in complex with 5-(2- thienyl)-3-isoxazolyl methanol
要素3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
キーワードLYASE / FATTY ACID BIOSYNTHESIS / BACTERIAL VIRULENCE / DRUG DISCOVERY
機能・相同性
機能・相同性情報


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / cytoplasm
類似検索 - 分子機能
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
(5-thiophen-2-ylisoxazol-3-yl)methanol / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
類似検索 - 構成要素
生物種PSEUDOMONAS AERUGINOSA (緑膿菌)
手法X線回折 / 分子置換 / 解像度: 2.5 Å
データ登録者Moynie, L. / McMahon, S.A. / Duthie, F.G. / Naismith, J.H.
引用ジャーナル: J.Mol.Biol. / : 2013
タイトル: Structural Insights Into the Mechanism and Inhibition of the Beta-Hydroxydecanoyl-Acyl Carrier Protein Dehydratase from Pseudomonas Aeruginosa
著者: Moynie, L. / Leckie, S.M. / Mcmahon, S.A. / Duthie, F.G. / Koehnke, A. / Taylor, J.W. / Alphey, M.S. / Brenk, R. / Smith, A.D. / Naismith, J.H.
履歴
登録2012年7月2日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02012年11月28日Provider: repository / タイプ: Initial release
改定 1.12013年1月30日Group: Database references
改定 1.22013年9月4日Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
改定 1.32018年6月13日Group: Data collection / Database references / カテゴリ: citation / Item: _citation.page_last
改定 1.42023年12月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
F: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
G: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
H: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
I: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
J: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
K: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
L: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
M: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
N: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
O: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
P: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
Q: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
R: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
S: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
T: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)378,99540
ポリマ-375,37120
非ポリマー3,62420
15,115839
1
S: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
T: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-18 kcal/mol
Surface area13530 Å2
手法PISA
2
C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-18.4 kcal/mol
Surface area13740 Å2
手法PISA
3
A: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-18.2 kcal/mol
Surface area13630 Å2
手法PISA
4
G: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
H: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-18.3 kcal/mol
Surface area13320 Å2
手法PISA
5
E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
F: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-18.3 kcal/mol
Surface area13970 Å2
手法PISA
6
M: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
N: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-18.4 kcal/mol
Surface area14240 Å2
手法PISA
7
O: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
P: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-17.8 kcal/mol
Surface area14100 Å2
手法PISA
8
K: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
L: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-17.7 kcal/mol
Surface area14370 Å2
手法PISA
9
I: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
J: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-18.2 kcal/mol
Surface area13910 Å2
手法PISA
10
Q: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
R: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8994
ポリマ-37,5372
非ポリマー3622
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-17.2 kcal/mol
Surface area13790 Å2
手法PISA
単位格子
Length a, b, c (Å)109.753, 108.170, 201.766
Angle α, β, γ (deg.)90.00, 103.22, 90.00
Int Tables number4
Space group name H-MP1211
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
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116A
216Q
117A
217R
118A
218S
119A
219T
120B
220C
121B
221D
122B
222E
123B
223F
124B
224G
125B
225H
126B
226I
127B
227J
128B
228K
129B
229L
130B
230M
131B
231N
132B
232O
133B
233P
134B
234Q
135B
235R
136B
236S
137B
237T
138C
238D
139C
239E
140C
240F
141C
241G
142C
242H
143C
243I
144C
244J
145C
245K
146C
246L
147C
247M
148C
248N
149C
249O
150C
250P
151C
251Q
152C
252R
153C
253S
154C
254T
155D
255E
156D
256F
157D
257G
158D
258H
159D
259I
160D
260J
161D
261K
162D
262L
163D
263M
164D
264N
165D
265O
166D
266P
167D
267Q
168D
268R
169D
269S
170D
270T
171E
271F
172E
272G
173E
273H
174E
274I
175E
275J
176E
276K
177E
277L
178E
278M
179E
279N
180E
280O
181E
281P
182E
282Q
183E
283R
184E
284S
185E
285T
186F
286G
187F
287H
188F
288I
189F
289J
190F
290K
191F
291L
192F
292M
193F
293N
194F
294O
195F
295P
196F
296Q
197F
297R
198F
298S
199F
299T
1100G
2100H
1101G
2101I
1102G
2102J
1103G
2103K
1104G
2104L
1105G
2105M
1106G
2106N
1107G
2107O
1108G
2108P
1109G
2109Q
1110G
2110R
1111G
2111S
1112G
2112T
1113H
2113I
1114H
2114J
1115H
2115K
1116H
2116L
1117H
2117M
1118H
2118N
1119H
2119O
1120H
2120P
1121H
2121Q
1122H
2122R
1123H
2123S
1124H
2124T
1125I
2125J
1126I
2126K
1127I
2127L
1128I
2128M
1129I
2129N
1130I
2130O
1131I
2131P
1132I
2132Q
1133I
2133R
1134I
2134S
1135I
2135T
1136J
2136K
1137J
2137L
1138J
2138M
1139J
2139N
1140J
2140O
1141J
2141P
1142J
2142Q
1143J
2143R
1144J
2144S
1145J
2145T
1146K
2146L
1147K
2147M
1148K
2148N
1149K
2149O
1150K
2150P
1151K
2151Q
1152K
2152R
1153K
2153S
1154K
2154T
1155L
2155M
1156L
2156N
1157L
2157O
1158L
2158P
1159L
2159Q
1160L
2160R
1161L
2161S
1162L
2162T
1163M
2163N
1164M
2164O
1165M
2165P
1166M
2166Q
1167M
2167R
1168M
2168S
1169M
2169T
1170N
2170O
1171N
2171P
1172N
2172Q
1173N
2173R
1174N
2174S
1175N
2175T
1176O
2176P
1177O
2177Q
1178O
2178R
1179O
2179S
1180O
2180T
1181P
2181Q
1182P
2182R
1183P
2183S
1184P
2184T
1185Q
2185R
1186Q
2186S
1187Q
2187T
1188R
2188S
1189R
2189T
1190S
2190T

NCSドメイン領域:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 2 - 171 / Label seq-ID: 2 - 171

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18AA
28II
19AA
29JJ
110AA
210KK
111AA
211LL
112AA
212MM
113AA
213NN
114AA
214OO
115AA
215PP
116AA
216QQ
117AA
217RR
118AA
218SS
119AA
219TT
120BB
220CC
121BB
221DD
122BB
222EE
123BB
223FF
124BB
224GG
125BB
225HH
126BB
226II
127BB
227JJ
128BB
228KK
129BB
229LL
130BB
230MM
131BB
231NN
132BB
232OO
133BB
233PP
134BB
234QQ
135BB
235RR
136BB
236SS
137BB
237TT
138CC
238DD
139CC
239EE
140CC
240FF
141CC
241GG
142CC
242HH
143CC
243II
144CC
244JJ
145CC
245KK
146CC
246LL
147CC
247MM
148CC
248NN
149CC
249OO
150CC
250PP
151CC
251QQ
152CC
252RR
153CC
253SS
154CC
254TT
155DD
255EE
156DD
256FF
157DD
257GG
158DD
258HH
159DD
259II
160DD
260JJ
161DD
261KK
162DD
262LL
163DD
263MM
164DD
264NN
165DD
265OO
166DD
266PP
167DD
267QQ
168DD
268RR
169DD
269SS
170DD
270TT
171EE
271FF
172EE
272GG
173EE
273HH
174EE
274II
175EE
275JJ
176EE
276KK
177EE
277LL
178EE
278MM
179EE
279NN
180EE
280OO
181EE
281PP
182EE
282QQ
183EE
283RR
184EE
284SS
185EE
285TT
186FF
286GG
187FF
287HH
188FF
288II
189FF
289JJ
190FF
290KK
191FF
291LL
192FF
292MM
193FF
293NN
194FF
294OO
195FF
295PP
196FF
296QQ
197FF
297RR
198FF
298SS
199FF
299TT
1100GG
2100HH
1101GG
2101II
1102GG
2102JJ
1103GG
2103KK
1104GG
2104LL
1105GG
2105MM
1106GG
2106NN
1107GG
2107OO
1108GG
2108PP
1109GG
2109QQ
1110GG
2110RR
1111GG
2111SS
1112GG
2112TT
1113HH
2113II
1114HH
2114JJ
1115HH
2115KK
1116HH
2116LL
1117HH
2117MM
1118HH
2118NN
1119HH
2119OO
1120HH
2120PP
1121HH
2121QQ
1122HH
2122RR
1123HH
2123SS
1124HH
2124TT
1125II
2125JJ
1126II
2126KK
1127II
2127LL
1128II
2128MM
1129II
2129NN
1130II
2130OO
1131II
2131PP
1132II
2132QQ
1133II
2133RR
1134II
2134SS
1135II
2135TT
1136JJ
2136KK
1137JJ
2137LL
1138JJ
2138MM
1139JJ
2139NN
1140JJ
2140OO
1141JJ
2141PP
1142JJ
2142QQ
1143JJ
2143RR
1144JJ
2144SS
1145JJ
2145TT
1146KK
2146LL
1147KK
2147MM
1148KK
2148NN
1149KK
2149OO
1150KK
2150PP
1151KK
2151QQ
1152KK
2152RR
1153KK
2153SS
1154KK
2154TT
1155LL
2155MM
1156LL
2156NN
1157LL
2157OO
1158LL
2158PP
1159LL
2159QQ
1160LL
2160RR
1161LL
2161SS
1162LL
2162TT
1163MM
2163NN
1164MM
2164OO
1165MM
2165PP
1166MM
2166QQ
1167MM
2167RR
1168MM
2168SS
1169MM
2169TT
1170NN
2170OO
1171NN
2171PP
1172NN
2172QQ
1173NN
2173RR
1174NN
2174SS
1175NN
2175TT
1176OO
2176PP
1177OO
2177QQ
1178OO
2178RR
1179OO
2179SS
1180OO
2180TT
1181PP
2181QQ
1182PP
2182RR
1183PP
2183SS
1184PP
2184TT
1185QQ
2185RR
1186QQ
2186SS
1187QQ
2187TT
1188RR
2188SS
1189RR
2189TT
1190SS
2190TT

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
183
184
185
186
187
188
189
190

NCS oper:
IDCodeMatrixベクター
1given(-0.2963, -0.0289, -0.9546), (-0.0286, -0.9988, 0.0391), (-0.9547, 0.0389, 0.2952)107.3987, -2.4652, 79.2715
2given(1, 0.0043, -0.0045), (-0.0044, 1, -0.0019), (0.0044, 0.0019, 1)-31.0966, -5.8387, -98.6554
3given(-0.2977, -0.03, -0.9542), (-0.0261, -0.9989, 0.0395), (-0.9543, 0.0366, 0.2966)210.977, 0.8159, 80.112
4given(0.3189, 0.0348, 0.9471), (0.0235, 0.9987, -0.0446), (-0.9475, 0.0365, 0.3177)-98.7059, 4.9777, 76.8772
5given(0.8101, -0.0716, -0.5819), (-0.0665, -0.9973, 0.0301), (-0.5825, 0.0143, -0.8127)63.0442, -1.7256, 196.3746
6given(0.3221, 0.0342, 0.9461), (0.0211, 0.9988, -0.0433), (-0.9465, 0.0339, 0.321)-202.309, 2.0296, 74.891
7given(0.8061, -0.0691, -0.5877), (-0.0665, -0.9974, 0.0261), (-0.588, 0.0181, -0.8087)96.4109, 4.7688, 294.3282
8given(0.2998, 0.0286, -0.9536), (0.0305, 0.9988, 0.0396), (0.9535, -0.041, 0.2986)104.6601, -4.3119, 70.7874
9given(-1, -0.0011, -0.0051), (0.0011, -1, 0.0029), (-0.0051, 0.0029, 1)9.064, 1.4186, 0.0925
10given(0.3012, 0.0319, -0.953), (0.0225, 0.9989, 0.0405), (0.9533, -0.0336, 0.3001)188.6739, -15.4589, 10.9634
11given(-0.9999, -0.0074, -0.0091), (0.0074, -1, -0.0009), (-0.0091, -0.001, 1)42.1685, 7.8803, -98.1618
12given(-0.3252, -0.0326, 0.9451), (-0.0225, -0.9989, -0.0421), (0.9454, -0.035, 0.3241)-95.8274, 6.5445, 68.1187
13given(-0.8057, 0.0741, -0.5877), (0.0711, 0.9971, 0.0283), (0.5881, -0.019, -0.8086)70.5703, -3.565, 191.1152
14given(-0.3223, -0.0336, 0.9461), (-0.0172, -0.999, -0.0413), (0.9465, -0.0296, 0.3214)-178.4929, 17.3975, 6.8018
15given(-0.8075, 0.0667, -0.5861), (0.0636, 0.9976, 0.0258), (0.5864, -0.0165, -0.8098)153.4229, -14.2489, 252.301
16given(0.8004, -0.0782, 0.5943), (-0.0839, -0.9963, -0.0181), (0.5935, -0.0354, -0.804)-62.8757, 3.7383, 190.6451
17given(-0.7974, 0.0842, 0.5976), (0.0811, 0.9962, -0.0322), (-0.598, 0.0228, -0.8012)-56.8141, 3.3853, 195.1425
18given(0.7987, -0.077, 0.5967), (-0.0752, -0.9968, -0.0278), (0.5969, -0.0226, -0.802)-147.0885, 16.5546, 250.318
19given(-0.7978, 0.0756, 0.5982), (0.0764, 0.9968, -0.0241), (-0.5981, 0.0265, -0.801)-90.7651, -4.1103, 293.0996

-
要素

#1: タンパク質
3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE / BETA-HYDROXYDECANOYL THIOESTER DEHYDRASE


分子量: 18768.533 Da / 分子数: 20 / 由来タイプ: 組換発現 / 由来: (組換発現) PSEUDOMONAS AERUGINOSA (緑膿菌) / : PA01 / プラスミド: PDEST14 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): TUNER / 参照: UniProt: O33877, EC: 4.2.1.60
#2: 化合物
ChemComp-3MQ / (5-thiophen-2-ylisoxazol-3-yl)methanol


分子量: 181.212 Da / 分子数: 20 / 由来タイプ: 合成 / : C8H7NO2S
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 839 / 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: 3.08 Å3/Da / 溶媒含有率: 60 % / 解説: NONE
結晶化pH: 4.5
詳細: 13% PEG MME 5000, 0.09 M LITHIUM SULPHATE, 0.1 MM SODIUM CITRATE PH 4.5

-
データ収集

回折平均測定温度: 100 K
放射光源由来: 回転陽極 / タイプ: RIGAKU MICROMAX / 波長: 1.54178
検出器タイプ: RIGAKU CCD / 検出器: CCD / 日付: 2011年6月11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: 1.54178 Å / 相対比: 1
反射解像度: 2.5→24 Å / Num. obs: 155181 / % possible obs: 96.9 % / 冗長度: 3.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.6
反射 シェル解像度: 2.5→2.54 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.26 / % possible all: 84.3

-
解析

ソフトウェア
名称バージョン分類
REFMAC5.6.0119精密化
HKL-2000データ削減
SCALEPACKデータスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 4FQ9
解像度: 2.5→23.95 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.894 / SU B: 17.525 / SU ML: 0.205 / 交差検証法: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.292 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
Rfactor反射数%反射Selection details
Rfree0.26509 7789 5 %RANDOM
Rwork0.23295 ---
obs0.23456 147156 96.88 %-
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: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.12 Å2
2---0.25 Å20 Å2
3---0.13 Å2
精密化ステップサイクル: LAST / 解像度: 2.5→23.95 Å
タンパク質核酸リガンド溶媒全体
原子数25965 0 240 839 27044
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01926830
X-RAY DIFFRACTIONr_bond_other_d0.0060.0218383
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.96936273
X-RAY DIFFRACTIONr_angle_other_deg1.1163.00144301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15753331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74123.2541183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.755154302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.56415189
X-RAY DIFFRACTIONr_chiral_restr0.0790.23864
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02130178
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025767
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)
11A61400.02
12B61400.02
21A61190.02
22C61190.02
31A61330.03
32D61330.03
41A60860.03
42E60860.03
51A61130.03
52F61130.03
61A61200.02
62G61200.02
71A61400.02
72H61400.02
81A61350.03
82I61350.03
91A60930.03
92J60930.03
101A61120.03
102K61120.03
111A61260.03
112L61260.03
121A61160.02
122M61160.02
131A60900.03
132N60900.03
141A61090.02
142O61090.02
151A60890.03
152P60890.03
161A60910.03
162Q60910.03
171A61090.02
172R61090.02
181A61050.03
182S61050.03
191A61470.02
192T61470.02
201B61320.03
202C61320.03
211B62490.03
212D62490.03
221B61190.03
222E61190.03
231B61960.03
232F61960.03
241B61180.02
242G61180.02
251B61570.02
252H61570.02
261B62240.03
262I62240.03
271B61260.03
272J61260.03
281B61860.04
282K61860.04
291B62410.03
292L62410.03
301B61310.03
302M61310.03
311B61670.03
312N61670.03
321B62320.02
322O62320.02
331B61930.04
332P61930.04
341B61210.03
342Q61210.03
351B61290.01
352R61290.01
361B61200.03
362S61200.03
371B61450.02
372T61450.02
381C61270.04
382D61270.04
391C60790.04
392E60790.04
401C61020.04
402F61020.04
411C60980.02
412G60980.02
421C61130.02
422H61130.02
431C61290.03
432I61290.03
441C60900.03
442J60900.03
451C61600.03
452K61600.03
461C61220.03
462L61220.03
471C61130.02
472M61130.02
481C60820.03
482N60820.03
491C60990.03
492O60990.03
501C60740.04
502P60740.04
511C61310.03
512Q61310.03
521C60740.03
522R60740.03
531C60800.03
532S60800.03
541C61230.02
542T61230.02
551D61210.04
552E61210.04
561D61990.04
562F61990.04
571D61170.03
572G61170.03
581D61560.02
582H61560.02
591D62220.03
592I62220.03
601D61270.04
602J61270.04
611D61710.05
612K61710.05
621D62330.04
622L62330.04
631D61300.03
632M61300.03
641D61640.04
642N61640.04
651D62200.04
652O62200.04
661D61990.04
662P61990.04
671D61210.04
672Q61210.04
681D61220.03
682R61220.03
691D61190.03
692S61190.03
701D61450.03
702T61450.03
711E61370.03
712F61370.03
721E60680.03
722G60680.03
731E61040.02
732H61040.02
741E61220.03
742I61220.03
751E61250.02
752J61250.02
761E60660.05
762K60660.05
771E61150.04
772L61150.04
781E61460.03
782M61460.03
791E61320.03
792N61320.03
801E61550.03
802O61550.03
811E61250.04
812P61250.04
821E60700.04
822Q60700.04
831E61240.03
832R61240.03
841E61280.03
842S61280.03
851E60900.03
852T60900.03
861F60880.03
862G60880.03
871F61280.03
872H61280.03
881F61940.04
882I61940.04
891F61450.03
892J61450.03
901F61480.05
902K61480.05
911F61810.04
912L61810.04
921F60990.04
922M60990.04
931F61410.04
932N61410.04
941F61670.04
942O61670.04
951F61440.04
952P61440.04
961F61030.04
962Q61030.04
971F60990.02
972R60990.02
981F60920.04
982S60920.04
991F61170.03
992T61170.03
1001G61180.02
1002H61180.02
1011G61180.02
1012I61180.02
1021G60750.03
1022J60750.03
1031G60880.03
1032K60880.03
1041G61060.03
1042L61060.03
1051G61050.02
1052M61050.02
1061G60880.02
1062N60880.02
1071G60910.03
1072O60910.03
1081G60590.04
1082P60590.04
1091G60630.04
1092Q60630.04
1101G60870.03
1102R60870.03
1111G60840.03
1112S60840.03
1121G61310
1122T61310
1131H61560.01
1132I61560.01
1141H61130.02
1142J61130.02
1151H61020.04
1152K61020.04
1161H61450.02
1162L61450.02
1171H61140.02
1172M61140.02
1181H61130.02
1182N61130.02
1191H61260.02
1192O61260.02
1201H61040.03
1202P61040.03
1211H61040.03
1212Q61040.03
1221H61250.02
1222R61250.02
1231H61260.02
1232S61260.02
1241H61460.02
1242T61460.02
1251I61290.02
1252J61290.02
1261I61760.04
1262K61760.04
1271I62210.03
1272L62210.03
1281I61310.03
1282M61310.03
1291I61740.01
1292N61740.01
1301I62020.03
1302O62020.03
1311I61610.04
1312P61610.04
1321I61180.04
1322Q61180.04
1331I61240.02
1332R61240.02
1341I61200.03
1342S61200.03
1351I61450.02
1352T61450.02
1361J60730.05
1362K60730.05
1371J61270.03
1372L61270.03
1381J60930.04
1382M60930.04
1391J60860.03
1392N60860.03
1401J61010.03
1402O61010.03
1411J60750.04
1412P60750.04
1421J61150.03
1422Q61150.03
1431J60760.03
1432R60760.03
1441J60800.03
1442S60800.03
1451J61000.03
1452T61000.03
1461K61600.05
1462L61600.05
1471K61000.04
1472M61000.04
1481K61190.04
1482N61190.04
1491K61500.04
1492O61500.04
1501K61140.05
1502P61140.05
1511K61280.04
1512Q61280.04
1521K60760.04
1522R60760.04
1531K60680.05
1532S60680.05
1541K61170.03
1542T61170.03
1551L61230.03
1552M61230.03
1561L61650.03
1562N61650.03
1571L62190.03
1572O62190.03
1581L61790.05
1582P61790.05
1591L61060.04
1592Q61060.04
1601L61090.03
1602R61090.03
1611L61120.03
1612S61120.03
1621L61290.03
1622T61290.03
1631M61410.03
1632N61410.03
1641M61650.03
1642O61650.03
1651M61330.03
1652P61330.03
1661M60730.04
1662Q60730.04
1671M61390.03
1672R61390.03
1681M61360.03
1682S61360.03
1691M61220.02
1692T61220.02
1701N62010.02
1702O62010.02
1711N61660.04
1712P61660.04
1721N60710.04
1722Q60710.04
1731N61350.02
1732R61350.02
1741N61350.03
1742S61350.03
1751N60980.02
1752T60980.02
1761O62200.04
1762P62200.04
1771O60920.03
1772Q60920.03
1781O61540
1782R61540
1791O61470.03
1792S61470.03
1801O61130.03
1802T61130.03
1811P60740.03
1812Q60740.03
1821P61310.02
1822R61310.02
1831P61280.04
1832S61280.04
1841P60890.04
1842T60890.04
1851Q60740.03
1852R60740.03
1861Q60710.04
1862S60710.04
1871Q60910.04
1872T60910.04
1881R61470.03
1882S61470.03
1891R61140.03
1892T61140.03
1901S61160.03
1902T61160.03
LS精密化 シェル解像度: 2.495→2.559 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.347 509 -
Rwork0.285 9931 -
obs--90.95 %
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)
15.38044.23171.55633.54470.56763.0422-0.50530.66520.5197-0.29640.39640.3299-0.36340.34680.10890.2173-0.1121-0.01280.24680.10780.286119.66718.25966.968
21.4023-0.24130.43270.6916-0.32460.6714-0.00650.0709-0.0165-0.1665-0.01410.0927-0.04570.1460.02060.1268-0.02480.02090.11870.010.146417.4896.90471.729
31.03820.74290.68862.3253-0.04020.6253-0.02950.0933-0.06720.11270.0986-0.0881-0.06230.0687-0.06910.0423-0.0030.03630.1384-0.02990.128718.7894.40977.877
44.4551-0.203-1.1893.5645-0.40191.94250.0083-0.20590.17060.16690.02590.19460.1014-0.1273-0.03410.0370.01620.03050.08220.0330.097211.8679.66480.467
52.73641.16580.27552.49780.83021.1381-0.004-0.13550.11660.1669-0.07050.108-0.0660.00240.07450.08250.00160.02030.10580.03290.106818.0136.84781.738
610.372-0.5240.86860.14410.589620.3434-0.02620.062-0.43770.0634-0.0071-0.23760.83460.73050.03330.26440.1224-0.04670.2399-0.01780.748238.873-18.09783.242
70.3748-0.22710.29510.77790.55271.18530.0410.08180.0172-0.0973-0.022-0.14980.01090.217-0.01890.07430.04420.08690.24360.03490.262632.93-6.28682.513
81.92480.5930.73233.10130.49650.9639-0.0617-0.0229-0.18440.08980.16740.21650.12910.0984-0.10570.05620.02450.02740.1238-0.00390.100225.262-8.74186.171
92.7682.1682-0.4652.9707-0.49134.37750.0647-0.0274-0.10540.23450.1451-0.06320.2899-0.1887-0.20980.07070.04090.01450.10390.00980.180326.722-10.16890.561
101.7879-0.51330.87531.0335-0.24972.10510.1106-0.0882-0.0240.1306-0.09590.02870.1579-0.1086-0.01460.10030.00790.07080.1635-0.01980.129623.795-6.72787.371
1116.18780.1522-0.3610.6938-2.48489.21370.03671.28271.33370.01130.0480.0225-0.40690.0491-0.08470.4345-0.1840.02020.18360.08630.219148.60324.021164.375
120.2926-0.13080.32031.185-0.28210.9597-0.0250.0772-0.0242-0.2005-0.0373-0.0389-0.02920.0770.06240.1333-0.04640.01960.1256-0.00630.06350.90612.459170.313
130.95250.75850.7225.05020.6780.6952-0.06470.0771-0.03390.06070.1590.1117-0.05620.1079-0.09430.0639-0.01590.0150.11070.0080.063549.66315.353178.578
141.71050.1722-0.30314.90742.30992.82980.0134-0.0553-0.0349-0.14070.2257-0.1672-0.238-0.1322-0.23910.0790.0013-0.00860.06490.05070.100143.32911.283176.523
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267.4641-3.8353-1.71911.98530.5727.1358-0.5241-0.5126-0.47770.25390.25660.23440.58740.52660.26750.26320.09650.00110.17020.00680.247638.803-17.994131.789
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3110.21797.4385-1.38245.4747-0.37819.934-0.36330.42460.0168-0.39270.4581-0.0633-0.95950.83-0.09480.3067-0.17770.04920.3513-0.0910.336279.35922.793203.839
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6220.89161.80084.7720.9151.92924.9589-0.1975-0.39731.77960.2766-0.0890.315-0.0977-0.11010.28650.6211-0.00490.35350.1943-0.05930.4144-28.69319.667133.371
630.3564-0.19620.04581.39640.35390.6196-0.0021-0.0258-0.00780.1918-0.010.0907-0.0656-0.07590.01210.10690.01020.05960.1350.00690.0506-26.65110.336125.121
641.83251.091-0.52535.2118-0.66221.9660.013-0.02890.10780.20850.1303-0.0620.1135-0.0082-0.14320.06060.0075-0.02990.1208-0.0210.0649-18.9045.164125.336
651.06052.4098-0.98237.2189-3.30673.98320.12390.1561-0.11840.06710.23390.02810.19250.0409-0.35780.12160.0235-0.01690.1016-0.02490.1669-17.3093.674125.292
661.801-0.8083-0.03456.4792.69761.1901-0.01770.77610.5285-0.2864-0.0284-0.3142-0.18070.10270.04610.3494-0.0519-0.08560.36510.15520.493-24.79819.25109.712
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680.27090.2847-0.23010.3162-0.2381.21330.0087-0.0167-0.0176-0.0047-0.05310.02340.0309-0.18250.04440.1107-0.0096-0.00520.1751-0.04010.1761-2.4382.111207.896
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741.0574-0.42360.48023.8499-1.20671.0494-0.034-0.1781-0.02930.06250.15540.01560.0461-0.0849-0.12140.12420.040.0020.0893-0.00950.028210.17910.417222.696
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763.8151-0.26782.0390.42340.04532.6195-0.37520.58450.4932-0.3264-0.1497-0.3571-0.14910.21660.52490.39760.03370.27920.25510.12590.45238.01524.231209.061
7712.510110.4058-11.83628.6703-9.866211.2304-1.836-0.0409-1.356-1.94490.2945-1.02942.24340.12331.54151.28610.2185-0.39850.4937-0.11061.1372-15.631-20.416140.732
781.84560.55380.32561.23440.18350.07490.0568-0.2982-0.06380.2532-0.08210.0340.0531-0.05650.02530.28960.01450.03210.24620.05180.0868-6.173-6.498145.386
792.2618-0.28351.09281.3171-0.44651.26470.08910.0588-0.2538-0.170.04970.06920.06050.0565-0.13880.13870.00630.0130.13770.03350.0658-3.044-6.033136.73
801.9148-2.20160.3414.03570.0580.2120.01190.09320.0681-0.1159-0.09440.14060-0.02710.08250.161-0.01120.01060.18720.00530.1202-7.6591.156133.631
813.5482-0.36311.08750.84711.43913.40090.35520.64060.0377-0.0418-0.1557-0.10830.27740.2975-0.19950.51420.21160.0210.56880.08940.426110.16-16.663136.43
827.91181.09451.3443.46292.08652.2386-0.3133-0.31130.480.17450.0489-0.0066-0.19070.05360.26440.24360.0246-0.05950.1599-0.04380.153914.918.843147.396
831.11330.0973-0.65190.3941-0.07491.07180.02-0.10790.07840.15730.0561-0.1274-0.0782-0.0017-0.07610.19250.0186-0.02830.18040.01910.099514.3692.873143.248
842.41030.13070.75475.77261.0550.647-0.04550.00540.0730.10960.0977-0.2021-0.0861-0.0781-0.05230.21860.04950.01930.1570.02940.06088.77212.899136.234
851.17040.1485-0.94615.3206-1.42082.339-0.08150.05170.0421-0.14180.1203-0.23450.07890.0297-0.03880.0483-0.01510.01080.11320.00130.062715.7142.93135.567
864.1019-1.9217-1.3095.39420.95582.43220.26250.23820.696-0.4615-0.1872-0.5718-0.2605-0.1051-0.07530.1978-0.03730.0020.17760.04720.16314.3810.818134.551
875.5924-0.42281.59750.2556-0.47611.03980.0273-0.7371-0.5529-0.02330.10230.00070.092-0.3592-0.12950.3247-0.034-0.01270.32420.13160.155226.117-7.806246.112
882.49160.61770.58460.6656-0.27550.9389-0.058-0.20090.13870.07840.0070.14030.15530.04690.05110.27760.0498-0.0080.15660.02080.118126.0715.639240.135
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900.67490.59870.33162.5977-0.08160.2464-0.13330.046-0.0113-0.17530.13050.3059-0.1034-0.03020.00280.31710.0683-0.09530.2095-0.03710.217823.3918.616232.437
916.5519-2.89623.26694.9874-5.17975.39830.2753-0.3789-0.2668-0.6509-0.2849-0.05970.63960.24270.00960.49110.0945-0.04190.297-0.00720.293341.009-8.904233.968
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941.61070.00840.21432.2410.29680.7773-0.0821-0.060.1006-0.01660.06290.032-0.1478-0.06850.01920.17680.04550.01290.146-0.00890.034541.92211.063237.674
951.8065-0.5445-0.33394.0026-0.6682.7807-0.01020.0850.0907-0.10580.1132-0.0713-0.1262-0.1809-0.10290.13010.01550.04860.1218-0.00040.084447.6211.423232.218
9612.9589-6.191-5.90096.5816.24345.92880.18310.07880.7738-0.1823-0.2028-0.0056-0.2186-0.20960.01970.49450.0728-0.09550.14670.04130.237831.41323.216234.1
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 21
2X-RAY DIFFRACTION2A22 - 71
3X-RAY DIFFRACTION3A72 - 121
4X-RAY DIFFRACTION4A122 - 146
5X-RAY DIFFRACTION5A147 - 171
6X-RAY DIFFRACTION6B2 - 14
7X-RAY DIFFRACTION7B15 - 86
8X-RAY DIFFRACTION8B87 - 118
9X-RAY DIFFRACTION9B119 - 141
10X-RAY DIFFRACTION10B142 - 171
11X-RAY DIFFRACTION11C2 - 14
12X-RAY DIFFRACTION12C15 - 86
13X-RAY DIFFRACTION13C87 - 118
14X-RAY DIFFRACTION14C119 - 158
15X-RAY DIFFRACTION15C159 - 171
16X-RAY DIFFRACTION16D2 - 10
17X-RAY DIFFRACTION17D11 - 66
18X-RAY DIFFRACTION18D67 - 111
19X-RAY DIFFRACTION19D112 - 141
20X-RAY DIFFRACTION20D142 - 171
21X-RAY DIFFRACTION21E2 - 14
22X-RAY DIFFRACTION22E15 - 109
23X-RAY DIFFRACTION23E110 - 140
24X-RAY DIFFRACTION24E141 - 159
25X-RAY DIFFRACTION25E160 - 171
26X-RAY DIFFRACTION26F2 - 18
27X-RAY DIFFRACTION27F19 - 50
28X-RAY DIFFRACTION28F51 - 121
29X-RAY DIFFRACTION29F122 - 144
30X-RAY DIFFRACTION30F145 - 171
31X-RAY DIFFRACTION31G2 - 14
32X-RAY DIFFRACTION32G15 - 109
33X-RAY DIFFRACTION33G110 - 141
34X-RAY DIFFRACTION34G142 - 159
35X-RAY DIFFRACTION35G160 - 171
36X-RAY DIFFRACTION36H2 - 19
37X-RAY DIFFRACTION37H20 - 66
38X-RAY DIFFRACTION38H67 - 131
39X-RAY DIFFRACTION39H132 - 160
40X-RAY DIFFRACTION40H161 - 171
41X-RAY DIFFRACTION41I2 - 15
42X-RAY DIFFRACTION42I16 - 83
43X-RAY DIFFRACTION43I84 - 129
44X-RAY DIFFRACTION44I130 - 146
45X-RAY DIFFRACTION45I147 - 171
46X-RAY DIFFRACTION46J2 - 14
47X-RAY DIFFRACTION47J15 - 109
48X-RAY DIFFRACTION48J110 - 140
49X-RAY DIFFRACTION49J141 - 159
50X-RAY DIFFRACTION50J160 - 171
51X-RAY DIFFRACTION51K2 - 171
52X-RAY DIFFRACTION52L2 - 14
53X-RAY DIFFRACTION53L15 - 108
54X-RAY DIFFRACTION54L109 - 138
55X-RAY DIFFRACTION55L139 - 158
56X-RAY DIFFRACTION56L159 - 171
57X-RAY DIFFRACTION57M2 - 17
58X-RAY DIFFRACTION58M18 - 50
59X-RAY DIFFRACTION59M51 - 113
60X-RAY DIFFRACTION60M114 - 147
61X-RAY DIFFRACTION61M148 - 171
62X-RAY DIFFRACTION62N2 - 14
63X-RAY DIFFRACTION63N15 - 109
64X-RAY DIFFRACTION64N110 - 136
65X-RAY DIFFRACTION65N139 - 160
66X-RAY DIFFRACTION66N161 - 171
67X-RAY DIFFRACTION67O2 - 14
68X-RAY DIFFRACTION68O15 - 77
69X-RAY DIFFRACTION69O78 - 121
70X-RAY DIFFRACTION70O122 - 144
71X-RAY DIFFRACTION71O145 - 171
72X-RAY DIFFRACTION72P2 - 14
73X-RAY DIFFRACTION73P15 - 100
74X-RAY DIFFRACTION74P101 - 131
75X-RAY DIFFRACTION75P132 - 158
76X-RAY DIFFRACTION76P159 - 171
77X-RAY DIFFRACTION77Q2 - 6
78X-RAY DIFFRACTION78Q7 - 76
79X-RAY DIFFRACTION79Q77 - 140
80X-RAY DIFFRACTION80Q141 - 160
81X-RAY DIFFRACTION81Q161 - 171
82X-RAY DIFFRACTION82R2 - 28
83X-RAY DIFFRACTION83R29 - 84
84X-RAY DIFFRACTION84R85 - 112
85X-RAY DIFFRACTION85R113 - 152
86X-RAY DIFFRACTION86R153 - 171
87X-RAY DIFFRACTION87S2 - 38
88X-RAY DIFFRACTION88S39 - 88
89X-RAY DIFFRACTION89S89 - 141
90X-RAY DIFFRACTION90S142 - 158
91X-RAY DIFFRACTION91S159 - 171
92X-RAY DIFFRACTION92T2 - 6
93X-RAY DIFFRACTION93T7 - 71
94X-RAY DIFFRACTION94T72 - 121
95X-RAY DIFFRACTION95T122 - 158
96X-RAY DIFFRACTION96T159 - 171

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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