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- PDB-2jkv: Structure of human Phosphogluconate Dehydrogenase in complex with... -

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基本情報

登録情報
データベース: PDB / ID: 2jkv
タイトルStructure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A
要素6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATINGホスホグルコン酸-2-デヒドロゲナーゼ
キーワードOXIDOREDUCTASE (酸化還元酵素) / PHOSPHOGLUCONATE / NADP (ニコチンアミドアデニンジヌクレオチドリン酸) / NADPH (ニコチンアミドアデニンジヌクレオチドリン酸) / PENTOSE SHUNT (ペントースリン酸経路) / DEHYDROGENASE (脱水素酵素)
機能・相同性
機能・相同性情報


D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose biosynthetic process / pentose-phosphate shunt, oxidative branch / ペントースリン酸経路 / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / NADP binding / extracellular exosome ...D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose biosynthetic process / pentose-phosphate shunt, oxidative branch / ペントースリン酸経路 / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / NADP binding / extracellular exosome / 細胞核 / 細胞質基質
類似検索 - 分子機能
6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / ホスホグルコン酸-2-デヒドロゲナーゼ / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase ...6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / ホスホグルコン酸-2-デヒドロゲナーゼ / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / ロスマンフォールド / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase, decarboxylating
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.532 Å
データ登録者Pilka, E.S. / Kavanagh, K.L. / von Delft, F. / Muniz, J.R.C. / Murray, J. / Picaud, S. / Guo, K. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Pilka, E.S. / Kavanagh, K.L. / von Delft, F. / Muniz, J.R.C. / Murray, J. / Picaud, S. / Guo, K. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Oppermann, U.
引用ジャーナル: To be Published
タイトル: Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A
著者: Ng, S.S. / von Delft, F. / Pilka, E.S. / Kavanagh, K.L. / McDonough, M.A. / Savitsky, P. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Schofield, C.J. / Oppermann, U.
履歴
登録2008年9月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02009年9月1日Provider: repository / タイプ: Initial release
改定 1.12015年1月14日Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
改定 1.22018年1月24日Group: Database references / カテゴリ: citation_author / Item: _citation_author.name
改定 1.32018年2月21日Group: Database references / カテゴリ: citation_author / Item: _citation_author.name
改定 1.42023年12月13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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
B: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
C: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
D: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
E: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
F: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)339,84134
ポリマ－334,5826
非ポリマー5,26028
水25,3111405
1
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
B: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)113,61114
ポリマ－111,5272
非ポリマー2,08412
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17120 Å2
ΔGint-207.6 kcal/mol
Surface area31720 Å2
手法PISA
2
C: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
D: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)113,4349
ポリマ－111,5272
非ポリマー1,9077
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-169.3 kcal/mol
Surface area31860 Å2
手法PISA
3
E: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
F: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)112,79711
ポリマ－111,5272
非ポリマー1,2699
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-178.1 kcal/mol
Surface area32350 Å2
手法PISA
単位格子
Length a, b, c (Å)56.643, 204.714, 170.319
Angle α, β, γ (deg.)90.00, 90.65, 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
11
21
31
41
51
61
12
22
32
42
52
62
13
23
33
43
53
63
14
24
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44
54
64
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35
45
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48
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69
110
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510
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113
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115
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435
535

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND BACKBONE AND (RESID 2:11 OR RESID 15:32...
211CHAIN B AND BACKBONE AND (RESID 2:11 OR RESID 15:32...
311CHAIN C AND BACKBONE AND (RESID 2:11 OR RESID 15:32...
411CHAIN D AND BACKBONE AND (RESID 2:11 OR RESID 15:32...
511CHAIN E AND BACKBONE AND (RESID 2:11 OR RESID 15:32...
611CHAIN F AND BACKBONE AND (RESID 2:11 OR RESID 15:32...
112CHAIN A AND SIDECHAIN AND (RESID 2:11 OR RESID 15:72 OR RESID 77:162 OR RESID 171: 182)
212CHAIN B AND SIDECHAIN AND (RESID 2:11 OR RESID 15:72 OR RESID 77:162 OR RESID 171: 182)
312CHAIN C AND SIDECHAIN AND (RESID 2:11 OR RESID 15:72 OR RESID 77:162 OR RESID 171: 182)
412CHAIN D AND SIDECHAIN AND (RESID 2:11 OR RESID 15:72 OR RESID 77:162 OR RESID 171: 182)
512CHAIN E AND SIDECHAIN AND (RESID 2:11 OR RESID 15:72 OR RESID 77:162 OR RESID 171: 182)
612CHAIN F AND SIDECHAIN AND (RESID 2:11 OR RESID 15:72 OR RESID 77:162 OR RESID 171: 182)
113CHAIN A AND BACKBONE AND (RESID 183:240 OR RESID 257:306)
213CHAIN B AND BACKBONE AND (RESID 183:240 OR RESID 257:306)
313CHAIN C AND BACKBONE AND (RESID 183:240 OR RESID 257:306)
413CHAIN D AND BACKBONE AND (RESID 183:240 OR RESID 257:306)
513CHAIN E AND BACKBONE AND (RESID 183:240 OR RESID 257:306)
613CHAIN F AND BACKBONE AND (RESID 183:240 OR RESID 257:306)
114CHAIN A AND SIDECHAIN AND (RESID 183:240 OR RESID 257:306)
214CHAIN B AND SIDECHAIN AND (RESID 183:240 OR RESID 257:306)
314CHAIN C AND SIDECHAIN AND (RESID 183:240 OR RESID 257:306)
414CHAIN D AND SIDECHAIN AND (RESID 183:240 OR RESID 257:306)
514CHAIN E AND SIDECHAIN AND (RESID 183:240 OR RESID 257:306)
614CHAIN F AND SIDECHAIN AND (RESID 183:240 OR RESID 257:306)
115CHAIN A AND BACKBONE AND RESID 316:361
215CHAIN B AND BACKBONE AND RESID 316:361
315CHAIN C AND BACKBONE AND RESID 316:361
415CHAIN D AND BACKBONE AND RESID 316:361
515CHAIN E AND BACKBONE AND RESID 316:361
615CHAIN F AND BACKBONE AND RESID 316:361
116CHAIN A AND SIDECHAIN AND RESID 316:361
216CHAIN B AND SIDECHAIN AND RESID 316:361
316CHAIN C AND SIDECHAIN AND RESID 316:361
416CHAIN D AND SIDECHAIN AND RESID 316:361
516CHAIN E AND SIDECHAIN AND RESID 316:361
616CHAIN F AND SIDECHAIN AND RESID 316:361
117CHAIN A AND BACKBONE AND RESID 373:385
217CHAIN B AND BACKBONE AND RESID 373:385
317CHAIN C AND BACKBONE AND RESID 373:385
417CHAIN D AND BACKBONE AND RESID 373:385
517CHAIN E AND BACKBONE AND RESID 373:385
617CHAIN F AND BACKBONE AND RESID 373:385
118CHAIN A AND SIDECHAIN AND RESID 373:385
218CHAIN B AND SIDECHAIN AND RESID 373:385
318CHAIN C AND SIDECHAIN AND RESID 373:385
418CHAIN D AND SIDECHAIN AND RESID 373:385
518CHAIN E AND SIDECHAIN AND RESID 373:385
618CHAIN F AND SIDECHAIN AND RESID 373:385
119CHAIN A AND BACKBONE AND RESID 386:434
219CHAIN B AND BACKBONE AND RESID 386:434
319CHAIN C AND BACKBONE AND RESID 386:434
419CHAIN D AND BACKBONE AND RESID 386:434
519CHAIN E AND BACKBONE AND RESID 386:434
619CHAIN F AND BACKBONE AND RESID 386:434
1110CHAIN A AND SIDECHAIN AND RESID 386:434
2110CHAIN B AND SIDECHAIN AND RESID 386:434
3110CHAIN C AND SIDECHAIN AND RESID 386:434
4110CHAIN D AND SIDECHAIN AND RESID 386:434
5110CHAIN E AND SIDECHAIN AND RESID 386:434
6110CHAIN F AND SIDECHAIN AND RESID 386:434
1111CHAIN A AND BACKBONE AND RESID 435:445
2111CHAIN B AND BACKBONE AND RESID 435:445
3111CHAIN C AND BACKBONE AND RESID 435:445
4111CHAIN D AND BACKBONE AND RESID 435:445
5111CHAIN E AND BACKBONE AND RESID 435:445
6111CHAIN F AND BACKBONE AND RESID 435:445
1112CHAIN A AND SIDECHAIN AND RESID 435:445
2112CHAIN B AND SIDECHAIN AND RESID 435:445
3112CHAIN C AND SIDECHAIN AND RESID 435:445
4112CHAIN D AND SIDECHAIN AND RESID 435:445
5112CHAIN E AND SIDECHAIN AND RESID 435:445
6112CHAIN F AND SIDECHAIN AND RESID 435:445
1113CHAIN A AND BACKBONE AND RESID 446:483
2113CHAIN B AND BACKBONE AND RESID 446:483
3113CHAIN C AND BACKBONE AND RESID 446:483
4113CHAIN D AND BACKBONE AND RESID 446:483
5113CHAIN E AND BACKBONE AND RESID 446:483
6113CHAIN F AND BACKBONE AND RESID 446:483
1114CHAIN A AND SIDECHAIN AND RESID 446:483
2114CHAIN B AND SIDECHAIN AND RESID 446:483
3114CHAIN C AND SIDECHAIN AND RESID 446:483
4114CHAIN D AND SIDECHAIN AND RESID 446:483
5114CHAIN E AND SIDECHAIN AND RESID 446:483
6114CHAIN F AND SIDECHAIN AND RESID 446:483
1115CHAIN A AND BACKBONE AND RESID 12:14
2115CHAIN B AND BACKBONE AND RESID 12:14
3115CHAIN C AND BACKBONE AND RESID 12:14
4115CHAIN D AND BACKBONE AND RESID 12:14
5115CHAIN F AND BACKBONE AND RESID 12:14
1116CHAIN A AND SIDECHAIN AND RESID 12:14
2116CHAIN B AND SIDECHAIN AND RESID 12:14
3116CHAIN C AND SIDECHAIN AND RESID 12:14
4116CHAIN D AND SIDECHAIN AND RESID 12:14
5116CHAIN F AND SIDECHAIN AND RESID 12:14
1117CHAIN A AND BACKBONE AND RESID 33:35
2117CHAIN B AND BACKBONE AND RESID 33:35
3117CHAIN C AND BACKBONE AND RESID 33:35
4117CHAIN D AND BACKBONE AND RESID 33:35
5117CHAIN F AND BACKBONE AND RESID 33:35
1118CHAIN A AND SIDECHAIN AND RESID 33:35
2118CHAIN B AND SIDECHAIN AND RESID 33:35
3118CHAIN C AND SIDECHAIN AND RESID 33:35
4118CHAIN D AND SIDECHAIN AND RESID 33:35
5118CHAIN F AND SIDECHAIN AND RESID 33:35
1119CHAIN A AND BACKBONE AND RESID 73:76
2119CHAIN B AND BACKBONE AND RESID 73:76
3119CHAIN C AND BACKBONE AND RESID 73:76
4119CHAIN D AND BACKBONE AND RESID 73:76
5119CHAIN F AND BACKBONE AND RESID 73:76
1120CHAIN A AND SIDECHAIN AND RESID 73:76
2120CHAIN B AND SIDECHAIN AND RESID 73:76
3120CHAIN C AND SIDECHAIN AND RESID 73:76
4120CHAIN D AND SIDECHAIN AND RESID 73:76
5120CHAIN F AND SIDECHAIN AND RESID 73:76
1121CHAIN A AND BACKBONE AND RESID 163:170
2121CHAIN B AND BACKBONE AND RESID 163:170
3121CHAIN C AND BACKBONE AND RESID 163:170
4121CHAIN D AND BACKBONE AND RESID 163:170
5121CHAIN E AND BACKBONE AND RESID 163:170
6121CHAIN F AND BACKBONE AND RESID 163:170
1122CHAIN A AND SIDECHAIN AND RESID 163:170
2122CHAIN B AND SIDECHAIN AND RESID 163:170
3122CHAIN C AND SIDECHAIN AND RESID 163:170
4122CHAIN D AND SIDECHAIN AND RESID 163:170
5122CHAIN E AND SIDECHAIN AND RESID 163:170
6122CHAIN F AND SIDECHAIN AND RESID 163:170
1123CHAIN A AND BACKBONE AND RESID 241:256
2123CHAIN B AND BACKBONE AND RESID 241:256
3123CHAIN C AND BACKBONE AND RESID 241:256
4123CHAIN D AND BACKBONE AND RESID 241:256
5123CHAIN E AND BACKBONE AND RESID 241:256
6123CHAIN F AND BACKBONE AND RESID 241:256
1124CHAIN A AND SIDECHAIN AND RESID 241:256
2124CHAIN B AND SIDECHAIN AND RESID 241:256
3124CHAIN C AND SIDECHAIN AND RESID 241:256
4124CHAIN D AND SIDECHAIN AND RESID 241:256
5124CHAIN E AND SIDECHAIN AND RESID 241:256
6124CHAIN F AND SIDECHAIN AND RESID 241:256
1125CHAIN A AND BACKBONE AND RESID 307:315
2125CHAIN B AND BACKBONE AND RESID 307:315
3125CHAIN C AND BACKBONE AND RESID 307:315
4125CHAIN D AND BACKBONE AND RESID 307:315
5125CHAIN E AND BACKBONE AND RESID 307:315
1126CHAIN A AND SIDECHAIN AND RESID 307:315
2126CHAIN B AND SIDECHAIN AND RESID 307:315
3126CHAIN C AND SIDECHAIN AND RESID 307:315
4126CHAIN D AND SIDECHAIN AND RESID 307:315
5126CHAIN E AND SIDECHAIN AND RESID 307:315
1127CHAIN A AND BACKBONE AND RESID 307:309
2127CHAIN F AND BACKBONE AND RESID 307:309
1128CHAIN A AND SIDECHAIN AND RESID 307:309
2128CHAIN F AND SIDECHAIN AND RESID 307:309
1129CHAIN A AND BACKBONE AND RESID 310:315
2129CHAIN B AND BACKBONE AND RESID 310:315
3129CHAIN C AND BACKBONE AND RESID 310:315
4129CHAIN D AND BACKBONE AND RESID 310:315
5129CHAIN E AND BACKBONE AND RESID 310:315
1130CHAIN A AND SIDECHAIN AND RESID 310:315
2130CHAIN B AND SIDECHAIN AND RESID 310:315
3130CHAIN C AND SIDECHAIN AND RESID 310:315
4130CHAIN D AND SIDECHAIN AND RESID 310:315
5130CHAIN E AND SIDECHAIN AND RESID 310:315
1131CHAIN A AND BACKBONE AND RESID 362:372
2131CHAIN B AND BACKBONE AND RESID 362:372
3131CHAIN C AND BACKBONE AND RESID 362:372
4131CHAIN F AND BACKBONE AND RESID 362:372
1132CHAIN A AND SIDECHAIN AND RESID 362:372
2132CHAIN B AND SIDECHAIN AND RESID 362:372
3132CHAIN C AND SIDECHAIN AND RESID 362:372
4132CHAIN F AND SIDECHAIN AND RESID 362:372
1133CHAIN D AND BACKBONE AND RESID 362:372
2133CHAIN E AND BACKBONE AND RESID 362:372
1134CHAIN D AND SIDECHAIN AND RESID 362:372
2134CHAIN E AND SIDECHAIN AND RESID 362:372
1135CHAIN A AND RESID 500
2135CHAIN B AND RESID 500
3135CHAIN C AND RESID 500
4135CHAIN D AND RESID 500
5135CHAIN E AND RESID 500

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
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要素

#1: タンパク質
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING / ホスホグルコン酸-2-デヒドロゲナーゼ


分子量: 55763.590 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PNIC28-BSA4 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: P52209, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: 化合物
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / ニコチンアミドアデニンジヌクレオチドリン酸


分子量: 743.405 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C21H28N7O17P3
#3: 化合物
ChemComp-CL / CHLORIDE ION / クロリド / 塩化物


分子量: 35.453 Da / 分子数: 11 / 由来タイプ: 合成 / 式: Cl
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン / 硫酸塩


分子量: 96.063 Da / 分子数: 12 / 由来タイプ: 合成 / 式: SO4
#5: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 1405 / 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: 2.93 Å3/Da / 溶媒含有率: 58 % / 解説: NONE
結晶化詳細: 0.20M NA2SO4, 20.0% PEG 3350, 10.0% ETGLY

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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: SLS / ビームライン: X10SA / 波長: 1
検出器タイプ: MARRESEARCH / 検出器: CCD / 日付: 2008年6月22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: 1 Å / 相対比: 1
反射解像度: 2.53→37 Å / Num. obs: 128646 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / 冗長度: 3.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.8
反射 シェル解像度: 2.53→2.67 Å / 冗長度: 2.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 87.1

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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
MOSFLMデータ削減
SCALA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 ENTRIES 1PGP, 1PGN

1pgp

1pgn


解像度: 2.532→36.899 Å / SU ML: 2.43 / σ(F): 0.01 / 位相誤差: 19.88 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2069 1982 1.7 %
Rwork0.1558 --
obs0.1566 118499 92.18 %
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 / Bsol: 34.474 Å2 / ksol: 0.321 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-1.7989 Å2-0 Å20.4807 Å2
2---3.2451 Å2-0 Å2
3---1.4461 Å2
精密化ステップサイクル: LAST / 解像度: 2.532→36.899 Å
タンパク質核酸リガンド溶媒全体
原子数22103 0 311 1405 23819
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00822886
X-RAY DIFFRACTIONf_angle_d1.06930950
X-RAY DIFFRACTIONf_dihedral_angle_d18.0428236
X-RAY DIFFRACTIONf_chiral_restr0.0743362
X-RAY DIFFRACTIONf_plane_restr0.0043963
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A648X-RAY DIFFRACTIONPOSITIONAL
12B648X-RAY DIFFRACTIONPOSITIONAL0.045
13C648X-RAY DIFFRACTIONPOSITIONAL0.046
14D648X-RAY DIFFRACTIONPOSITIONAL0.051
15E648X-RAY DIFFRACTIONPOSITIONAL0.053
16F648X-RAY DIFFRACTIONPOSITIONAL0.045
21A568X-RAY DIFFRACTIONPOSITIONAL
22B568X-RAY DIFFRACTIONPOSITIONAL0.546
23C563X-RAY DIFFRACTIONPOSITIONAL0.569
24D567X-RAY DIFFRACTIONPOSITIONAL0.478
25E565X-RAY DIFFRACTIONPOSITIONAL0.542
26F571X-RAY DIFFRACTIONPOSITIONAL0.519
31A428X-RAY DIFFRACTIONPOSITIONAL
32B428X-RAY DIFFRACTIONPOSITIONAL0.041
33C432X-RAY DIFFRACTIONPOSITIONAL0.046
34D432X-RAY DIFFRACTIONPOSITIONAL0.051
35E432X-RAY DIFFRACTIONPOSITIONAL0.057
36F432X-RAY DIFFRACTIONPOSITIONAL0.043
41A387X-RAY DIFFRACTIONPOSITIONAL
42B387X-RAY DIFFRACTIONPOSITIONAL0.395
43C395X-RAY DIFFRACTIONPOSITIONAL0.511
44D391X-RAY DIFFRACTIONPOSITIONAL0.632
45E393X-RAY DIFFRACTIONPOSITIONAL0.551
46F395X-RAY DIFFRACTIONPOSITIONAL0.4
51A184X-RAY DIFFRACTIONPOSITIONAL
52B184X-RAY DIFFRACTIONPOSITIONAL0.039
53C184X-RAY DIFFRACTIONPOSITIONAL0.041
54D184X-RAY DIFFRACTIONPOSITIONAL0.066
55E184X-RAY DIFFRACTIONPOSITIONAL0.067
56F184X-RAY DIFFRACTIONPOSITIONAL0.04
61A179X-RAY DIFFRACTIONPOSITIONAL
62B179X-RAY DIFFRACTIONPOSITIONAL0.192
63C183X-RAY DIFFRACTIONPOSITIONAL0.447
64D183X-RAY DIFFRACTIONPOSITIONAL0.675
65E183X-RAY DIFFRACTIONPOSITIONAL0.676
66F183X-RAY DIFFRACTIONPOSITIONAL0.78
71A52X-RAY DIFFRACTIONPOSITIONAL
72B52X-RAY DIFFRACTIONPOSITIONAL0.032
73C52X-RAY DIFFRACTIONPOSITIONAL0.042
74D52X-RAY DIFFRACTIONPOSITIONAL0.061
75E52X-RAY DIFFRACTIONPOSITIONAL0.07
76F52X-RAY DIFFRACTIONPOSITIONAL0.034
81A53X-RAY DIFFRACTIONPOSITIONAL
82B53X-RAY DIFFRACTIONPOSITIONAL0.193
83C47X-RAY DIFFRACTIONPOSITIONAL0.292
84D53X-RAY DIFFRACTIONPOSITIONAL0.489
85E50X-RAY DIFFRACTIONPOSITIONAL0.618
86F53X-RAY DIFFRACTIONPOSITIONAL0.215
91A196X-RAY DIFFRACTIONPOSITIONAL
92B196X-RAY DIFFRACTIONPOSITIONAL0.038
93C196X-RAY DIFFRACTIONPOSITIONAL0.041
94D196X-RAY DIFFRACTIONPOSITIONAL0.052
95E196X-RAY DIFFRACTIONPOSITIONAL0.059
96F196X-RAY DIFFRACTIONPOSITIONAL0.045
101A192X-RAY DIFFRACTIONPOSITIONAL
102B192X-RAY DIFFRACTIONPOSITIONAL0.514
103C189X-RAY DIFFRACTIONPOSITIONAL0.438
104D185X-RAY DIFFRACTIONPOSITIONAL0.662
105E192X-RAY DIFFRACTIONPOSITIONAL0.719
106F189X-RAY DIFFRACTIONPOSITIONAL0.361
111A44X-RAY DIFFRACTIONPOSITIONAL
112B44X-RAY DIFFRACTIONPOSITIONAL0.039
113C44X-RAY DIFFRACTIONPOSITIONAL0.046
114D44X-RAY DIFFRACTIONPOSITIONAL0.036
115E44X-RAY DIFFRACTIONPOSITIONAL0.047
116F44X-RAY DIFFRACTIONPOSITIONAL0.047
121A39X-RAY DIFFRACTIONPOSITIONAL
122B39X-RAY DIFFRACTIONPOSITIONAL0.217
123C39X-RAY DIFFRACTIONPOSITIONAL0.295
124D39X-RAY DIFFRACTIONPOSITIONAL0.335
125E39X-RAY DIFFRACTIONPOSITIONAL0.291
126F39X-RAY DIFFRACTIONPOSITIONAL0.261
131A152X-RAY DIFFRACTIONPOSITIONAL
132B152X-RAY DIFFRACTIONPOSITIONAL0.037
133C152X-RAY DIFFRACTIONPOSITIONAL0.049
134D152X-RAY DIFFRACTIONPOSITIONAL0.04
135E152X-RAY DIFFRACTIONPOSITIONAL0.038
136F108X-RAY DIFFRACTIONPOSITIONAL0.043
141A145X-RAY DIFFRACTIONPOSITIONAL
142B145X-RAY DIFFRACTIONPOSITIONAL0.609
143C145X-RAY DIFFRACTIONPOSITIONAL0.707
144D145X-RAY DIFFRACTIONPOSITIONAL0.481
145E144X-RAY DIFFRACTIONPOSITIONAL0.605
146F112X-RAY DIFFRACTIONPOSITIONAL0.65
151A12X-RAY DIFFRACTIONPOSITIONAL
152B12X-RAY DIFFRACTIONPOSITIONAL0.035
153C12X-RAY DIFFRACTIONPOSITIONAL0.026
154D12X-RAY DIFFRACTIONPOSITIONAL0.04
155F12X-RAY DIFFRACTIONPOSITIONAL0.046
161A8X-RAY DIFFRACTIONPOSITIONAL
162B8X-RAY DIFFRACTIONPOSITIONAL0.086
163C8X-RAY DIFFRACTIONPOSITIONAL0.123
164D8X-RAY DIFFRACTIONPOSITIONAL0.16
165F8X-RAY DIFFRACTIONPOSITIONAL0.193
171A12X-RAY DIFFRACTIONPOSITIONAL
172B12X-RAY DIFFRACTIONPOSITIONAL0.02
173C12X-RAY DIFFRACTIONPOSITIONAL0.025
174D12X-RAY DIFFRACTIONPOSITIONAL0.021
175F12X-RAY DIFFRACTIONPOSITIONAL0.029
181A14X-RAY DIFFRACTIONPOSITIONAL
182B14X-RAY DIFFRACTIONPOSITIONAL0.087
183C14X-RAY DIFFRACTIONPOSITIONAL0.136
184D14X-RAY DIFFRACTIONPOSITIONAL0.066
185F14X-RAY DIFFRACTIONPOSITIONAL0.126
191A16X-RAY DIFFRACTIONPOSITIONAL
192B16X-RAY DIFFRACTIONPOSITIONAL0.044
193C16X-RAY DIFFRACTIONPOSITIONAL0.038
194D16X-RAY DIFFRACTIONPOSITIONAL0.05
195F16X-RAY DIFFRACTIONPOSITIONAL0.035
201A16X-RAY DIFFRACTIONPOSITIONAL
202B16X-RAY DIFFRACTIONPOSITIONAL0.185
203C16X-RAY DIFFRACTIONPOSITIONAL0.212
204D16X-RAY DIFFRACTIONPOSITIONAL0.27
205F16X-RAY DIFFRACTIONPOSITIONAL0.208
211A32X-RAY DIFFRACTIONPOSITIONAL
212B32X-RAY DIFFRACTIONPOSITIONAL0.029
213C32X-RAY DIFFRACTIONPOSITIONAL0.07
214D32X-RAY DIFFRACTIONPOSITIONAL0.049
215E32X-RAY DIFFRACTIONPOSITIONAL0.049
216F32X-RAY DIFFRACTIONPOSITIONAL0.038
221A19X-RAY DIFFRACTIONPOSITIONAL
222B19X-RAY DIFFRACTIONPOSITIONAL0.778
223C19X-RAY DIFFRACTIONPOSITIONAL0.599
224D19X-RAY DIFFRACTIONPOSITIONAL0.846
225E19X-RAY DIFFRACTIONPOSITIONAL0.744
226F19X-RAY DIFFRACTIONPOSITIONAL0.785
231A64X-RAY DIFFRACTIONPOSITIONAL
232B64X-RAY DIFFRACTIONPOSITIONAL0.058
233C64X-RAY DIFFRACTIONPOSITIONAL0.035
234D64X-RAY DIFFRACTIONPOSITIONAL0.039
235E64X-RAY DIFFRACTIONPOSITIONAL0.036
236F64X-RAY DIFFRACTIONPOSITIONAL0.055
241A68X-RAY DIFFRACTIONPOSITIONAL
242B68X-RAY DIFFRACTIONPOSITIONAL0.512
243C67X-RAY DIFFRACTIONPOSITIONAL0.303
244D64X-RAY DIFFRACTIONPOSITIONAL0.258
245E66X-RAY DIFFRACTIONPOSITIONAL0.313
246F68X-RAY DIFFRACTIONPOSITIONAL0.624
251A36X-RAY DIFFRACTIONPOSITIONAL
252B36X-RAY DIFFRACTIONPOSITIONAL0.021
253C36X-RAY DIFFRACTIONPOSITIONAL0.028
254D36X-RAY DIFFRACTIONPOSITIONAL0.028
255E36X-RAY DIFFRACTIONPOSITIONAL0.031
261A25X-RAY DIFFRACTIONPOSITIONAL
262B25X-RAY DIFFRACTIONPOSITIONAL0.207
263C25X-RAY DIFFRACTIONPOSITIONAL0.179
264D29X-RAY DIFFRACTIONPOSITIONAL0.285
265E25X-RAY DIFFRACTIONPOSITIONAL0.194
271A12X-RAY DIFFRACTIONPOSITIONAL
272F12X-RAY DIFFRACTIONPOSITIONAL0.061
281A9X-RAY DIFFRACTIONPOSITIONAL
282F9X-RAY DIFFRACTIONPOSITIONAL0.199
291A24X-RAY DIFFRACTIONPOSITIONAL
292B24X-RAY DIFFRACTIONPOSITIONAL0.011
293C24X-RAY DIFFRACTIONPOSITIONAL0.014
294D24X-RAY DIFFRACTIONPOSITIONAL0.021
295E24X-RAY DIFFRACTIONPOSITIONAL0.014
301A20X-RAY DIFFRACTIONPOSITIONAL
302B20X-RAY DIFFRACTIONPOSITIONAL0.119
303C20X-RAY DIFFRACTIONPOSITIONAL0.192
304D20X-RAY DIFFRACTIONPOSITIONAL0.09
305E20X-RAY DIFFRACTIONPOSITIONAL0.094
311A44X-RAY DIFFRACTIONPOSITIONAL
312B44X-RAY DIFFRACTIONPOSITIONAL0.037
313C44X-RAY DIFFRACTIONPOSITIONAL0.04
314F44X-RAY DIFFRACTIONPOSITIONAL0.043
321A46X-RAY DIFFRACTIONPOSITIONAL
322B46X-RAY DIFFRACTIONPOSITIONAL0.206
323C46X-RAY DIFFRACTIONPOSITIONAL0.721
324F46X-RAY DIFFRACTIONPOSITIONAL0.507
331D44X-RAY DIFFRACTIONPOSITIONAL
332E44X-RAY DIFFRACTIONPOSITIONAL0.037
341D46X-RAY DIFFRACTIONPOSITIONAL
342E46X-RAY DIFFRACTIONPOSITIONAL0.341
351A48X-RAY DIFFRACTIONPOSITIONAL
352B48X-RAY DIFFRACTIONPOSITIONAL0.038
353C48X-RAY DIFFRACTIONPOSITIONAL0.038
354D48X-RAY DIFFRACTIONPOSITIONAL0.033
355E48X-RAY DIFFRACTIONPOSITIONAL0.042
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.532-2.59530.28591250.23256198X-RAY DIFFRACTION69
2.5953-2.66550.2661170.22557087X-RAY DIFFRACTION79
2.6655-2.74390.29251360.20977605X-RAY DIFFRACTION85
2.7439-2.83240.26271460.20028113X-RAY DIFFRACTION89
2.8324-2.93360.24261350.18488173X-RAY DIFFRACTION92
2.9336-3.0510.251370.18818373X-RAY DIFFRACTION93
3.051-3.18980.25521540.18548572X-RAY DIFFRACTION95
3.1898-3.35790.23161370.16788704X-RAY DIFFRACTION96
3.3579-3.56810.20751660.14798800X-RAY DIFFRACTION98
3.5681-3.84330.17891410.12748878X-RAY DIFFRACTION99
3.8433-4.22960.15721500.11248918X-RAY DIFFRACTION99
4.2296-4.84040.13431560.09949011X-RAY DIFFRACTION99
4.8404-6.0940.15771440.12858991X-RAY DIFFRACTION99
6.094-36.90310.17421380.13799094X-RAY DIFFRACTION99
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.15970.2294-0.32221.67030.15382.10830.0968-0.01950.020.4709-0.1466-0.1089-0.623-0.11440.0480.34380.0384-0.07240.0515-0.00070.058925.290826.9736-25.4801
20.2729-0.34510.18931.50020.05370.0252-0.01170.09170.049-0.0953-0.0945-0.18820.02560.09970.07060.02950.04040.01970.10070.04510.029834.70687.6426-47.773
3-0.00550.69690.1160.3706-0.1234-1.1053-0.1943-0.2226-0.0693-0.3184-0.1645-0.05750.02210.29590.30270.57780.40130.04210.5475-0.05270.093938.1169-6.5336-65.7327
4-0.5065-0.18780.10171.6839-0.46820.77090.09590.0973-0.0591-0.2283-0.13220.35390.03480.12150.0067-0.03650.03250.00460.1808-0.00830.082818.04286.2934-44.6408
52.752-0.13280.16481.0197-1.06750.99820.4220.44540.3939-0.0234-0.20860.3054-0.1102-0.2081-0.18190.10240.05360.03350.07590.02910.044619.624317.1664-45.5719
63.9504-0.61980.44160.8305-0.42150.99190.3181-0.3273-0.7037-0.1139-0.20870.3066-0.10320.0522-0.05930.04820.0272-0.0620.1223-0.02870.19636.314410.4625-44.1372
71.0215-0.07840.33591.3384-0.49340.2535-0.09230.0372-0.1538-0.3030.04690.1960.10130.003-0.01780.12240.0829-0.05480.1786-0.02490.054920.087-2.6666-52.5615
8-1.4577-1.08580.48611.96790.20531.8055-0.1458-0.19370.05080.0158-0.23870.91240.0872-0.25480.18570.05580.0148-0.09220.1511-0.04170.251916.1075-19.1208-40.9528
90.4749-0.1875-0.21831.6882-0.09990.4478-0.28120.0325-0.36410.16270.16860.3681-0.0038-0.10930.06410.0413-0.00130.0480.1023-0.02910.26615.9143-26.0592-28.0461
100.09720.26210.18070.5678-0.2278-0.28720.2833-0.18030.05380.1554-0.03860.228-0.0342-0.1515-0.01120.36090.05180.1460.19770.07870.248221.7508-20.7328-15.9066
110.7083-0.12130.01942.48570.03720.7956-0.0164-0.0127-0.00270.84230.0310.09590.07290.0613-0.04160.34220.0656-0.0060.0525-0.00610.028432.4019-23.8665-10.0316
120.0192-0.3857-0.23461.5448-0.38940.38910.00990.1232-0.1138-0.04920.01020.140.0186-0.0959-0.02190.04580.0346-0.03480.1161-0.05350.109623.2725-20.2094-39.5444
13-0.97240.0396-0.6235-1.2069-1.55263.4821-0.31570.3827-0.0648-0.6184-0.12530.17780.00291.1604-0.35410.53870.0416-0.37340.6712-0.2476-0.074820.6548-18.6669-62.4109
14-0.4403-0.247-0.32951.0674-0.50440.07230.1415-0.0893-0.10960.1844-0.4835-0.4503-0.00950.0722-0.6445-0.07770.17750.07430.0414-0.07550.060440.0308-16.9275-37.2651
155.19521.7513-0.70972.4038-1.27930.67990.3851-0.0371-0.7927-0.0952-0.5776-0.29920.20230.09730.01360.01840.0024-0.0730.04250.02340.086338.2924-26.6273-32.2419
16-1.1108-4.6401-0.32324.962-0.00042.98490.0110.04440.1806-0.0548-0.1039-0.95040.39550.67770.11570.13430.05340.04740.16240.00520.208251.623-20.3055-34.7601
171.5397-0.6335-0.50281.5821-0.31710.2407-0.05860.08220.1066-0.3538-0.0836-0.13390.1048-0.05980.09050.15040.08290.03460.1527-0.01580.060937.9731-14.0531-49.0714
180.2569-0.28960.44850.7315-0.46230.58210.0508-0.16960.1579-0.0586-0.3774-0.1877-0.14830.37210.26850.04340.1380.0240.14990.16220.163441.94646.0449-48.4548
19-0.2585-0.1080.55771.2768-0.22311.346-0.19820.10.2960.1345-0.0576-0.3501-0.19710.4010.21960.03690.0113-0.00710.13420.10060.192741.899119.0152-41.629
200.1182-0.3451-0.52940.1515-0.175-0.01050.1148-0.0654-0.1441-0.2627-0.5075-0.16040.15690.14180.30910.3407-0.0153-0.11470.18330.05340.380535.968421.286-28.5572
211.21930.0924-0.41751.1252-0.31470.55270.1233-0.117-0.08290.1351-0.0870.00650.27820.0704-0.03560.4481-0.0110.00340.1819-0.03410.034321.243321.714185.6484
220.4998-0.25320.02891.28330.69980.43520.09250.15470.013-0.4459-0.05250.1874-0.05670.0219-0.01640.28350.0043-0.01230.1597-0.0764-0.02356.566348.10679.5534
23-0.3732-0.39591.79582.4046-1.5824-1.70580.0341-0.06970.2054-0.6311-0.3378-0.4596-0.2337-0.15050.32711.0620.3755-0.06750.61290.17190.5889-1.113168.517972.0614
240.0945-0.151-0.06020.58530.26550.0525-0.03580.00760.2617-0.16470.1005-0.1191-0.45260.09960.01470.45750.0270.04330.1757-0.1007-0.048623.487949.832178.69
250.57780.4787-0.31740.4117-0.29580.5460.34050.2278-0.28580.162-0.1062-0.315-0.76320.0834-0.20950.3972-0.01820.03360.1972-0.12320.084621.603540.787772.9792
260.35630.36441.2280.68080.63751.8580.1733-0.14610.07770.10420.3101-0.291-0.14240.002-0.02690.4602-0.0640.0830.2127-0.16670.117734.917247.466574.5044
270.02860.28960.32140.72930.15030.4897-0.0236-0.02940.1283-0.41920.1649-0.002-0.4302-0.01-0.04610.6050.04640.0970.1849-0.07510.049219.445961.075777.2183
280.27180.4710.1644-0.303-1.41841.7267-0.0509-0.0578-0.1511-0.67280.5782-0.7702-0.62440.1189-0.42330.5447-0.06760.1820.1581-0.10370.262326.973170.303793.8627
290.3939-0.71650.2763-0.1443-1.11220.299-0.3279-0.06740.08670.2990.1601-0.1494-0.3123-0.04180.12640.6224-0.06210.09780.2587-0.12440.380730.858770.258107.9664
300.43760.16610.0695-0.08680.09270.09050.28470.0419-0.2785-0.2913-0.1172-0.1823-0.22070.0556-0.0980.5995-0.01430.04380.4245-0.09970.548228.628959.2815117.2105
311.39320.1057-0.13240.68080.60111.292-0.06830.0321-0.05620.1604-0.0052-0.12850.0344-0.09910.05140.4132-0.0050.08610.0316-0.02210.092320.059157.8484126.1798
320.5233-0.69790.08360.66230.7611.7832-0.0901-0.03270.252-0.14990.0633-0.194-0.5295-0.05190.0220.4443-0.03220.04840.0798-0.07010.128220.45869.484797.4291
331.2773-1.0408-0.76890.83190.95641.0883-0.29930.40670.08870.00150.0572-0.0752-0.1073-0.34630.19921.54570.03340.15710.4250.10670.3216.891379.121576.744
34-0.09020.06460.22522.8385-0.33831.98680.02570.07640.00080.3271-0.4398-0.1761-0.4981-0.35310.28710.38450.05610.06640.1715-0.10070.18395.006163.6288101.9198
350.0914-0.57380.20850.9897-0.9977-2.16520.3110.05260.1915-0.8918-0.08970.1279-0.2324-0.0186-0.16750.52120.03970.06670.2038-0.07540.10318.73269.7314110.2867
36-0.38210.2840.96350.5015-0.9588-1.4988-0.2057-0.2133-0.0019-0.26830.11570.0395-0.3059-0.67390.16520.85230.20820.08860.4959-0.12850.3356-4.623964.2458108.8851
37-0.08020.302-0.0591.10021.10740.1899-0.05190.0053-0.0061-0.6002-0.10330.086-0.3521-0.11750.11350.45690.1501-0.02810.1923-0.05910.11423.572567.103990.1666
380.52170.17230.6311-0.086-0.3795-0.8174-0.3125-0.0482-0.13660.0329-0.0417-0.05890.1647-0.6270.31280.36170.02720.05190.3181-0.09420.0922-0.554248.885181.6759
390.331-0.2039-0.21320.61890.05360.27130.0796-0.0896-0.0310.1198-0.16530.07070.2631-0.0430.04240.2796-0.0143-0.07720.2689-0.10440.11531.108934.426380.7454
400.9985-0.34590.53520.55-0.31560.13820.2702-0.2603-0.1316-0.09270.1139-0.1104-0.1724-0.1916-0.26140.5534-0.10050.07330.3306-0.03890.191410.291726.89288.8888
410.92-0.5523-0.07412.9384-0.59931.66510.11580.04920.0444-0.6674-0.2699-0.13030.45820.07330.0940.3612-0.00910.07340.04410.01860.058725.1777-10.509125.4348
420.09270.32-0.30611.3567-0.47960.5526-0.0737-0.0741-0.1147-0.0871-0.0274-0.12560.09250.07170.10260.0716-0.01710.02340.09420.03760.033135.92899.138648.1591
43-1.4309-1.56590.0313-1.4266-0.58170.3345-0.2962-0.1090.1697-0.0395-0.27460.3104-0.83160.26950.3260.489-0.1666-0.21060.6611-0.25440.272138.735422.923166.4268
440.11520.2942-0.16741.38480.64071.3326-0.0284-0.06310.12570.1289-0.02940.2710.20050.13690.01370.0747-0.01960.03740.06250.01980.055219.171510.794544.7421
453.42223.37493.79720.8086-2.3128.23490.3312-0.376-0.33750.38330.1839-0.3092-0.362-0.5456-0.13540.1203-0.0075-0.0220.0735-0.05430.075821.4508-0.061245.6052
460.9521-0.79110.21551.36291.15792.54270.27740.3339-0.02810.5005-0.39670.36390.6299-0.27670.29190.4153-0.14380.16940.2067-0.05840.12938.39286.017645.1064
470.7126-0.1448-0.08810.6702-0.0664-0.503-0.05-0.0140.0680.26140.06580.0495-0.16380.0408-0.01340.2033-0.07650.05470.1532-0.01930.058721.241219.689352.7332
480.40471.75630.54924.6168-1.04182.89320.00070.04890.2762-0.3256-0.01250.5981-0.10120.414-0.10320.0202-0.00180.00620.0601-0.01610.061617.379135.954240.7477
490.64590.24310.92522.23440.95681.8093-0.30070.09320.1462-0.44040.05780.0801-0.212-0.08790.22070.1056-0.0373-0.01680.03890.00640.110717.489342.645227.7761
500.6168-0.4597-0.26480.22040.0095-0.14430.1698-0.0617-0.34660.05230.02020.51490.1232-0.0381-0.03110.3325-0.0667-0.07780.07490.02510.142723.284337.15815.8127
510.9347-0.1638-0.03061.15060.04540.73290.09010.020.021-0.6422-0.00170.0209-0.15620.1143-0.09310.3883-0.08390.01570.0747-0.01530.047434.0140.09859.9836
520.52370.2184-0.22730.5204-0.40860.7152-0.0324-0.04670.04110.01920.016-0.0138-0.0665-0.05130.01310.1332-0.01620.02370.1027-0.03280.071224.658336.810139.336
530.1793-0.0791-0.1335-0.2831-2.85680.81310.0638-0.38070.07950.8243-0.17820.0625-0.71310.005-0.1730.39060.01840.13590.2165-0.09730.048521.345834.958462.7415
54-0.3621-0.03040.170.7146-0.69630.68560.0495-0.1131-0.0430.0464-0.1901-0.1517-0.27410.29660.01560.0923-0.08680.00760.125-0.03810.118241.332433.608437.4169
550.4776-0.29470.06640.0656-0.43020.14160.03740.17020.37170.1683-0.0408-0.2501-0.20540.175-0.01630.207-0.09720.10780.117-0.02310.142839.782143.099132.0278
560.460.2920.42111.1389-0.47660.9368-0.02470.0401-0-0.4579-0.11470.00320.00690.20120.01720.2333-0.08550.00840.2107-0.05590.149852.989536.813834.6422
571.64240.25590.05970.8419-0.77940.0586-0.1288-0.0449-0.10270.24660.0158-0.1175-0.30850.06730.08940.2118-0.1195-0.01680.2006-0.04690.075439.209130.795749.0164
58-0.0717-0.7289-0.4760.9828-0.6291.60630.0346-0.1590.07580.0181-0.4519-0.30510.22980.29320.25590.07720.00110.04750.20490.05220.134443.178410.693948.9436
592.8791.0529-1.94260.5979-1.93172.5863-0.5038-0.0646-0.5687-0.5773-0.048-0.49450.636-0.02250.50530.13160.03040.13530.05240.04250.295143.7061-1.995144.5946
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 2:182
2X-RAY DIFFRACTION2CHAIN A AND RESID 183:306
3X-RAY DIFFRACTION3CHAIN A AND RESID 307:315
4X-RAY DIFFRACTION4CHAIN A AND RESID 316:361
5X-RAY DIFFRACTION5CHAIN A AND RESID 362:372
6X-RAY DIFFRACTION6CHAIN A AND RESID 373:385
7X-RAY DIFFRACTION7CHAIN A AND RESID 386:434
8X-RAY DIFFRACTION8CHAIN A AND RESID 435:445
9X-RAY DIFFRACTION9CHAIN A AND RESID 446:483
10X-RAY DIFFRACTION10CHAIN A AND RESID 500
11X-RAY DIFFRACTION11CHAIN B AND RESID 2:182
12X-RAY DIFFRACTION12CHAIN B AND RESID 183:306
13X-RAY DIFFRACTION13CHAIN B AND RESID 307:315
14X-RAY DIFFRACTION14CHAIN B AND RESID 316:361
15X-RAY DIFFRACTION15CHAIN B AND RESID 362:372
16X-RAY DIFFRACTION16CHAIN B AND RESID 373:385
17X-RAY DIFFRACTION17CHAIN B AND RESID 386:434
18X-RAY DIFFRACTION18CHAIN B AND RESID 435:445
19X-RAY DIFFRACTION19CHAIN B AND RESID 446:483
20X-RAY DIFFRACTION20CHAIN B AND RESID 500
21X-RAY DIFFRACTION21CHAIN C AND RESID 2:182
22X-RAY DIFFRACTION22CHAIN C AND RESID 183:306
23X-RAY DIFFRACTION23CHAIN C AND RESID 307:315
24X-RAY DIFFRACTION24CHAIN C AND RESID 316:361
25X-RAY DIFFRACTION25CHAIN C AND RESID 362:372
26X-RAY DIFFRACTION26CHAIN C AND RESID 373:385
27X-RAY DIFFRACTION27CHAIN C AND RESID 386:434
28X-RAY DIFFRACTION28CHAIN C AND RESID 435:445
29X-RAY DIFFRACTION29CHAIN C AND RESID 446:483
30X-RAY DIFFRACTION30CHAIN C AND RESID 500
31X-RAY DIFFRACTION31CHAIN D AND RESID 2:182
32X-RAY DIFFRACTION32CHAIN D AND RESID 183:306
33X-RAY DIFFRACTION33CHAIN D AND RESID 307:315
34X-RAY DIFFRACTION34CHAIN D AND RESID 316:361
35X-RAY DIFFRACTION35CHAIN D AND RESID 362:372
36X-RAY DIFFRACTION36CHAIN D AND RESID 373:385
37X-RAY DIFFRACTION37CHAIN D AND RESID 386:434
38X-RAY DIFFRACTION38CHAIN D AND RESID 435:445
39X-RAY DIFFRACTION39CHAIN D AND RESID 446:483
40X-RAY DIFFRACTION40CHAIN D AND RESID 500
41X-RAY DIFFRACTION41CHAIN E AND RESID 2:182
42X-RAY DIFFRACTION42CHAIN E AND RESID 183:306
43X-RAY DIFFRACTION43CHAIN E AND RESID 307:315
44X-RAY DIFFRACTION44CHAIN E AND RESID 316:361
45X-RAY DIFFRACTION45CHAIN E AND RESID 362:372
46X-RAY DIFFRACTION46CHAIN E AND RESID 373:385
47X-RAY DIFFRACTION47CHAIN E AND RESID 386:434
48X-RAY DIFFRACTION48CHAIN E AND RESID 435:445
49X-RAY DIFFRACTION49CHAIN E AND RESID 446:483
50X-RAY DIFFRACTION50CHAIN E AND RESID 500
51X-RAY DIFFRACTION51CHAIN F AND RESID 2:182
52X-RAY DIFFRACTION52CHAIN F AND RESID 183:306
53X-RAY DIFFRACTION53CHAIN F AND RESID 307:315
54X-RAY DIFFRACTION54CHAIN F AND RESID 316:361
55X-RAY DIFFRACTION55CHAIN F AND RESID 362:372
56X-RAY DIFFRACTION56CHAIN F AND RESID 373:385
57X-RAY DIFFRACTION57CHAIN F AND RESID 386:434
58X-RAY DIFFRACTION58CHAIN F AND RESID 435:445
59X-RAY DIFFRACTION59CHAIN F AND RESID 446:483

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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