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- PDB-4cq6: The crystal structure of the allene oxide cyclase 2 from Arabidop... -

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基本情報

登録情報
データベース: PDB / ID: 4cq6
タイトルThe crystal structure of the allene oxide cyclase 2 from Arabidopsis thaliana with bound inhibitor - vernolic acid
要素ALLENE OXIDE CYCLASE 2, CHLOROPLASTIC
キーワードISOMERASE / JASMONATES / CYCLIZATION / OXYLIPINS
機能・相同性
機能・相同性情報


allene-oxide cyclase / allene-oxide cyclase activity / stromule / jasmonic acid biosynthetic process / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / response to cold / chloroplast / cytosol
類似検索 - 分子機能
AOC barrel-like / Allene oxide cyclase-like / Allene oxide cyclase / Allene oxide cyclase superfamily / Allene oxide cyclase / Allene oxide cyclase/Dirigent protein / Beta Barrel / Mainly Beta
類似検索 - ドメイン・相同性
PHOSPHATE ION / Chem-T25 / Allene oxide cyclase 2, chloroplastic
類似検索 - 構成要素
生物種ARABIDOPSIS THALIANA (シロイヌナズナ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.8 Å
データ登録者Terlecka, B.A. / Pollmann, S. / Hofmann, E.
引用ジャーナル: To be Published
タイトル: The Ligand-Bound Structures of the Aoc2 from A. Thaliana and the Implications for the Catalytic Mechanism
著者: Terlecka, B.A. / Pollmann, S. / Hofmann, E.
履歴
登録2014年2月11日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02015年3月4日Provider: repository / タイプ: Initial release
改定 2.02019年10月23日Group: Atomic model / Data collection / Other / カテゴリ: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
改定 2.12023年12月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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構造の表示

構造ビューア分子:
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集合体

登録構造単位
A: ALLENE OXIDE CYCLASE 2, CHLOROPLASTIC
B: ALLENE OXIDE CYCLASE 2, CHLOROPLASTIC
C: ALLENE OXIDE CYCLASE 2, CHLOROPLASTIC
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,3857
ポリマ－62,5793
非ポリマー8064
水10,647591
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-40.2 kcal/mol
Surface area20690 Å2
手法PISA
単位格子
Length a, b, c (Å)64.600, 99.900, 106.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34
15
25
35
16
26
36
17
27
37
18
28
38
19
29
39
110
210
310
111
211
311
112
212
312
113
213
313
114
214
314
115
215
315
116
216
316
117
217
317
118
218
318
119
219
319
120
220
320
121
221
321
122
222
322
123
223
323
124
224
324
125
225
325
126
226
326
127
227
327
128
228
328
129
229
329
130
230
330
131
231
331
132
232
332

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 76:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
211CHAIN B AND (RESSEQ 76:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
311CHAIN C AND (RESSEQ 76:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
112CHAIN A AND (RESSEQ 76:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
212CHAIN B AND (RESSEQ 76:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
312CHAIN C AND (RESSEQ 76:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
113CHAIN A AND (RESSEQ 166:174 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
213CHAIN B AND (RESSEQ 166:174 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
313CHAIN C AND (RESSEQ 166:174 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
114CHAIN A AND (RESSEQ 166:174 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
214CHAIN B AND (RESSEQ 166:174 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
314CHAIN C AND (RESSEQ 166:174 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
115CHAIN A AND (RESSEQ 176:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
215CHAIN B AND (RESSEQ 176:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
315CHAIN C AND (RESSEQ 176:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
116CHAIN A AND (RESSEQ 176:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
216CHAIN B AND (RESSEQ 176:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
316CHAIN C AND (RESSEQ 176:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
117CHAIN A AND (RESSEQ 16:23 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
217CHAIN B AND (RESSEQ 16:23 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
317CHAIN C AND (RESSEQ 16:23 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
118CHAIN A AND (RESSEQ 16:23 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
218CHAIN B AND (RESSEQ 16:23 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
318CHAIN C AND (RESSEQ 16:23 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
119CHAIN A AND (RESSEQ 25:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
219CHAIN B AND (RESSEQ 25:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
319CHAIN C AND (RESSEQ 25:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1110CHAIN A AND (RESSEQ 25:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2110CHAIN B AND (RESSEQ 25:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3110CHAIN C AND (RESSEQ 25:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1111CHAIN A AND (RESSEQ 28:34 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2111CHAIN B AND (RESSEQ 28:34 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3111CHAIN C AND (RESSEQ 28:34 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1112CHAIN A AND (RESSEQ 28:34 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2112CHAIN B AND (RESSEQ 28:34 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3112CHAIN C AND (RESSEQ 28:34 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1113CHAIN A AND (RESSEQ 43:61 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2113CHAIN B AND (RESSEQ 43:61 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3113CHAIN C AND (RESSEQ 43:61 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1114CHAIN A AND (RESSEQ 43:61 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2114CHAIN B AND (RESSEQ 43:61 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3114CHAIN C AND (RESSEQ 43:61 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1115CHAIN A AND (RESSEQ 63:74 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2115CHAIN B AND (RESSEQ 63:74 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3115CHAIN C AND (RESSEQ 63:74 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1116CHAIN A AND (RESSEQ 63:74 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2116CHAIN B AND (RESSEQ 63:74 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3116CHAIN C AND (RESSEQ 63:74 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1117CHAIN A AND (RESSEQ 76:79 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2117CHAIN B AND (RESSEQ 76:79 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3117CHAIN C AND (RESSEQ 76:79 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1118CHAIN A AND (RESSEQ 76:79 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2118CHAIN B AND (RESSEQ 76:79 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3118CHAIN C AND (RESSEQ 76:79 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1119CHAIN A AND (RESSEQ 81:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2119CHAIN B AND (RESSEQ 81:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3119CHAIN C AND (RESSEQ 81:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1120CHAIN A AND (RESSEQ 81:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2120CHAIN B AND (RESSEQ 81:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3120CHAIN C AND (RESSEQ 81:101 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1121CHAIN A AND (RESSEQ 103:129 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2121CHAIN B AND (RESSEQ 103:129 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3121CHAIN C AND (RESSEQ 103:129 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1122CHAIN A AND (RESSEQ 103:129 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2122CHAIN B AND (RESSEQ 103:129 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3122CHAIN C AND (RESSEQ 103:129 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1123CHAIN A AND (RESSEQ 133:154 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2123CHAIN B AND (RESSEQ 133:154 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3123CHAIN C AND (RESSEQ 133:154 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1124CHAIN A AND (RESSEQ 133:154 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2124CHAIN B AND (RESSEQ 133:154 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3124CHAIN C AND (RESSEQ 133:154 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1125CHAIN A AND (RESSEQ 166:172 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2125CHAIN B AND (RESSEQ 166:172 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3125CHAIN C AND (RESSEQ 166:172 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1126CHAIN A AND (RESSEQ 166:172 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2126CHAIN B AND (RESSEQ 166:172 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3126CHAIN C AND (RESSEQ 166:172 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1127CHAIN A AND (RESSEQ 176:177 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2127CHAIN B AND (RESSEQ 176:177 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3127CHAIN C AND (RESSEQ 176:177 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1128CHAIN A AND (RESSEQ 176:177 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2128CHAIN B AND (RESSEQ 176:177 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3128CHAIN C AND (RESSEQ 176:177 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1129CHAIN A AND (RESSEQ 179:183 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2129CHAIN B AND (RESSEQ 179:183 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3129CHAIN C AND (RESSEQ 179:183 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1130CHAIN A AND (RESSEQ 179:183 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2130CHAIN B AND (RESSEQ 179:183 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3130CHAIN C AND (RESSEQ 179:183 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
1131CHAIN A AND (RESSEQ 185:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
2131CHAIN B AND (RESSEQ 185:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
3131CHAIN C AND (RESSEQ 185:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND BACKBONE
1132CHAIN A AND (RESSEQ 185:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
2132CHAIN B AND (RESSEQ 185:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN
3132CHAIN C AND (RESSEQ 185:188 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D) AND SIDECHAIN

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

NCS oper:
IDCodeMatrixベクター
1given(-0.4833, -0.8685, 0.1098), (0.8557, -0.4952, -0.1505), (0.185, 0.0212, 0.9825)-29.8894, -40.156, 1.215
2given(-0.4921, 0.8524, 0.177), (-0.862, -0.5054, 0.0373), (0.1213, -0.1342, 0.9835)19.7504, -46.3499, -3.48

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要素

#1: タンパク質 ALLENE OXIDE CYCLASE 2, CHLOROPLASTIC


分子量: 20859.670 Da / 分子数: 3 / 断片: RESIDUE 78-253 / 由来タイプ: 組換発現
由来: (組換発現) ARABIDOPSIS THALIANA (シロイヌナズナ)
プラスミド: PQE30 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): ER2566 / 参照: UniProt: Q9LS02, allene-oxide cyclase
#2: 化合物 ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / (4R)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#3: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 1 / 由来タイプ: 合成 / 式: PO4
#4: 化合物 ChemComp-T25 / (9Z)-11-[(2R,3S)-3-pentyloxiran-2-yl]undec-9-enoic acid / 12R,13S-epoxy-9(Z)-octadecenoic acid / 12α,13α-エポキシオレイン酸


分子量: 296.445 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C18H32O3
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 591 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.7 Å3/Da / 溶媒含有率: 55 % / 解説: NONE
結晶化pH: 4.2 / 詳細: 0.2 M LI2SO4, 0.1 M PI-CITRATE PH 4.2, 20% PEG1000

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID23-2 / 波長: 0.872
検出器タイプ: MARRESEARCH / 検出器: CCD / 日付: 2010年11月30日 / 詳細: MIRRORS
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.872 Å / 相対比: 1
反射解像度: 1.8→20 Å / Num. obs: 64212 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / 冗長度: 7.4 % / Biso Wilson estimate: 14.18 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.2
反射 シェル解像度: 1.8→1.85 Å / 冗長度: 7.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.8 / % possible all: 99.3

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 2DIO

2dio


解像度: 1.8→19.958 Å / SU ML: 0.13 / σ(F): 2 / 位相誤差: 14 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1586 3212 5 %
Rwork0.1305 --
obs0.132 64209 99.76 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 19.3 Å2
精密化ステップサイクル: LAST / 解像度: 1.8→19.958 Å
タンパク質核酸リガンド溶媒全体
原子数4092 0 55 591 4738
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0144344
X-RAY DIFFRACTIONf_angle_d1.4395903
X-RAY DIFFRACTIONf_dihedral_angle_d14.8111626
X-RAY DIFFRACTIONf_chiral_restr0.069645
X-RAY DIFFRACTIONf_plane_restr0.009759
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A104X-RAY DIFFRACTIONPOSITIONAL
12B104X-RAY DIFFRACTIONPOSITIONAL0.083
13C103X-RAY DIFFRACTIONPOSITIONAL0.14
21A114X-RAY DIFFRACTIONPOSITIONAL
22B114X-RAY DIFFRACTIONPOSITIONAL0.219
23C110X-RAY DIFFRACTIONPOSITIONAL0.24
31A36X-RAY DIFFRACTIONPOSITIONAL
32B36X-RAY DIFFRACTIONPOSITIONAL0.165
33C36X-RAY DIFFRACTIONPOSITIONAL0.141
41A31X-RAY DIFFRACTIONPOSITIONAL
42B31X-RAY DIFFRACTIONPOSITIONAL0.692
43C31X-RAY DIFFRACTIONPOSITIONAL0.654
51A52X-RAY DIFFRACTIONPOSITIONAL
52B52X-RAY DIFFRACTIONPOSITIONAL0.098
53C51X-RAY DIFFRACTIONPOSITIONAL0.098
61A44X-RAY DIFFRACTIONPOSITIONAL
62B44X-RAY DIFFRACTIONPOSITIONAL0.663
63C40X-RAY DIFFRACTIONPOSITIONAL0.723
71A32X-RAY DIFFRACTIONPOSITIONAL
72B32X-RAY DIFFRACTIONPOSITIONAL0.136
73C32X-RAY DIFFRACTIONPOSITIONAL0.055
81A35X-RAY DIFFRACTIONPOSITIONAL
82B35X-RAY DIFFRACTIONPOSITIONAL0.339
83C35X-RAY DIFFRACTIONPOSITIONAL0.116
91A8X-RAY DIFFRACTIONPOSITIONAL
92B8X-RAY DIFFRACTIONPOSITIONAL0.044
93C8X-RAY DIFFRACTIONPOSITIONAL0.049
101A9X-RAY DIFFRACTIONPOSITIONAL
102B9X-RAY DIFFRACTIONPOSITIONAL0.054
103C9X-RAY DIFFRACTIONPOSITIONAL0.076
111A28X-RAY DIFFRACTIONPOSITIONAL
112B28X-RAY DIFFRACTIONPOSITIONAL0.102
113C28X-RAY DIFFRACTIONPOSITIONAL0.103
121A31X-RAY DIFFRACTIONPOSITIONAL
122B31X-RAY DIFFRACTIONPOSITIONAL0.195
123C31X-RAY DIFFRACTIONPOSITIONAL0.193
131A76X-RAY DIFFRACTIONPOSITIONAL
132B76X-RAY DIFFRACTIONPOSITIONAL0.094
133C76X-RAY DIFFRACTIONPOSITIONAL0.134
141A72X-RAY DIFFRACTIONPOSITIONAL
142B72X-RAY DIFFRACTIONPOSITIONAL0.166
143C72X-RAY DIFFRACTIONPOSITIONAL0.2
151A48X-RAY DIFFRACTIONPOSITIONAL
152B48X-RAY DIFFRACTIONPOSITIONAL0.061
153C48X-RAY DIFFRACTIONPOSITIONAL0.068
161A34X-RAY DIFFRACTIONPOSITIONAL
162B34X-RAY DIFFRACTIONPOSITIONAL0.095
163C34X-RAY DIFFRACTIONPOSITIONAL0.103
171A16X-RAY DIFFRACTIONPOSITIONAL
172B16X-RAY DIFFRACTIONPOSITIONAL0.043
173C16X-RAY DIFFRACTIONPOSITIONAL0.068
181A17X-RAY DIFFRACTIONPOSITIONAL
182B17X-RAY DIFFRACTIONPOSITIONAL0.139
183C17X-RAY DIFFRACTIONPOSITIONAL0.16
191A84X-RAY DIFFRACTIONPOSITIONAL
192B84X-RAY DIFFRACTIONPOSITIONAL0.083
193C83X-RAY DIFFRACTIONPOSITIONAL0.111
201A92X-RAY DIFFRACTIONPOSITIONAL
202B92X-RAY DIFFRACTIONPOSITIONAL0.219
203C88X-RAY DIFFRACTIONPOSITIONAL0.144
211A108X-RAY DIFFRACTIONPOSITIONAL
212B108X-RAY DIFFRACTIONPOSITIONAL0.12
213C108X-RAY DIFFRACTIONPOSITIONAL0.075
221A90X-RAY DIFFRACTIONPOSITIONAL
222B90X-RAY DIFFRACTIONPOSITIONAL0.187
223C90X-RAY DIFFRACTIONPOSITIONAL0.128
231A88X-RAY DIFFRACTIONPOSITIONAL
232B88X-RAY DIFFRACTIONPOSITIONAL0.201
233C88X-RAY DIFFRACTIONPOSITIONAL0.101
241A97X-RAY DIFFRACTIONPOSITIONAL
242B97X-RAY DIFFRACTIONPOSITIONAL0.314
243C97X-RAY DIFFRACTIONPOSITIONAL0.186
251A28X-RAY DIFFRACTIONPOSITIONAL
252B28X-RAY DIFFRACTIONPOSITIONAL0.135
253C28X-RAY DIFFRACTIONPOSITIONAL0.113
261A25X-RAY DIFFRACTIONPOSITIONAL
262B25X-RAY DIFFRACTIONPOSITIONAL0.311
263C25X-RAY DIFFRACTIONPOSITIONAL0.214
271A8X-RAY DIFFRACTIONPOSITIONAL
272B8X-RAY DIFFRACTIONPOSITIONAL0.02
273C8X-RAY DIFFRACTIONPOSITIONAL0.041
281A5X-RAY DIFFRACTIONPOSITIONAL
282B5X-RAY DIFFRACTIONPOSITIONAL0.048
283C5X-RAY DIFFRACTIONPOSITIONAL0.022
291A20X-RAY DIFFRACTIONPOSITIONAL
292B20X-RAY DIFFRACTIONPOSITIONAL0.06
293C20X-RAY DIFFRACTIONPOSITIONAL0.084
301A12X-RAY DIFFRACTIONPOSITIONAL
302B12X-RAY DIFFRACTIONPOSITIONAL0.12
303C12X-RAY DIFFRACTIONPOSITIONAL0.129
311A16X-RAY DIFFRACTIONPOSITIONAL
312B16X-RAY DIFFRACTIONPOSITIONAL0.058
313C15X-RAY DIFFRACTIONPOSITIONAL0.092
321A20X-RAY DIFFRACTIONPOSITIONAL
322B20X-RAY DIFFRACTIONPOSITIONAL0.098
323C16X-RAY DIFFRACTIONPOSITIONAL0.155
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.826900.16542735X-RAY DIFFRACTION100
1.8269-1.855400.16312761X-RAY DIFFRACTION99
1.8554-1.88580.19544080.15542325X-RAY DIFFRACTION100
1.8858-1.918300.15312742X-RAY DIFFRACTION99
1.9183-1.953100.14342756X-RAY DIFFRACTION100
1.9531-1.99070.17123660.14122395X-RAY DIFFRACTION100
1.9907-2.031300.12372733X-RAY DIFFRACTION99
2.0313-2.07540.15223340.12442447X-RAY DIFFRACTION100
2.0754-2.123600.12452763X-RAY DIFFRACTION100
2.1236-2.17660.1672660.12472498X-RAY DIFFRACTION100
2.1766-2.23540.1563390.11712730X-RAY DIFFRACTION100
2.2354-2.30110.15412690.11212517X-RAY DIFFRACTION100
2.3011-2.375300.11972774X-RAY DIFFRACTION100
2.3753-2.460.15462650.12172503X-RAY DIFFRACTION100
2.46-2.558300.12622793X-RAY DIFFRACTION100
2.5583-2.67450.15162200.13112568X-RAY DIFFRACTION100
2.6745-2.81510.16191760.1292632X-RAY DIFFRACTION100
2.8151-2.9910.16631580.14022639X-RAY DIFFRACTION100
2.991-3.2210.15331540.13882684X-RAY DIFFRACTION100
3.221-3.54350.15911200.13542709X-RAY DIFFRACTION100
3.5435-4.05260.14891000.11162754X-RAY DIFFRACTION100
4.0526-5.09170.11531560.10412707X-RAY DIFFRACTION100
5.0917-19.95880.19151810.16662832X-RAY DIFFRACTION100

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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://pdbjlvh1.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