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- PDB-6x91: Crystal structure of MBP-fused human APOBEC1 -

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基本情報

登録情報
データベース: PDB / ID: 6x91
タイトルCrystal structure of MBP-fused human APOBEC1
要素Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
キーワードHYDROLASE / APOBEC / RNA editing / deamination / metalloenzyme
機能・相同性
機能・相同性情報


positive regulation of mRNA modification / mRNA(cytosine6666) deaminase / cytosine deaminase activity / mRNA Editing: C to U Conversion / Formation of the Editosome / mRNA modification / DNA cytosine deamination / response to xenobiotic stimulus => GO:0009410 / cytidine to uridine editing / cytidine deaminase activity ...positive regulation of mRNA modification / mRNA(cytosine6666) deaminase / cytosine deaminase activity / mRNA Editing: C to U Conversion / Formation of the Editosome / mRNA modification / DNA cytosine deamination / response to xenobiotic stimulus => GO:0009410 / cytidine to uridine editing / cytidine deaminase activity / : / negative regulation of DNA methylation-dependent heterochromatin formation / response to osmotic stress / detection of maltose stimulus / response to zinc ion / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / RNA processing / ribonucleoprotein complex binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / enzyme activator activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / lipid metabolic process / mRNA processing / response to calcium ion / cellular response to insulin stimulus / outer membrane-bounded periplasmic space / response to ethanol / defense response to virus / periplasmic space / protein domain specific binding / mRNA binding / DNA damage response / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm
類似検索 - 分子機能
C->U-editing enzyme APOBEC-1 / APOBEC4-like -AID/APOBEC-deaminase / APOBEC-like C-terminal domain / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site ...C->U-editing enzyme APOBEC-1 / APOBEC4-like -AID/APOBEC-deaminase / APOBEC-like C-terminal domain / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
類似検索 - ドメイン・相同性
alpha-maltose / CACODYLATE ION / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein / C->U-editing enzyme APOBEC-1
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.51 Å
データ登録者Wolfe, A.D. / Li, S.-X. / Chen, X.S.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 米国
引用ジャーナル: NAR Cancer / 年: 2020
タイトル: The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity.
著者: Wolfe, A.D. / Li, S. / Goedderz, C. / Chen, X.S.
履歴
登録2020年6月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年12月9日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
B: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
C: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
D: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
E: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
F: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
G: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
H: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)542,99838
ポリマ－536,5868
非ポリマー6,41130
水00
1
A: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
B: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,5789
ポリマ－134,1472
非ポリマー1,4327
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
D: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,92110
ポリマ－134,1472
非ポリマー1,7748
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
F: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,5789
ポリマ－134,1472
非ポリマー1,4327
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
H: Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,92110
ポリマ－134,1472
非ポリマー1,7748
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)177.715, 179.209, 210.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 2 through 92 or resid 94...
21(chain E and (resid 2 through 92 or resid 94...
12(chain B and (resid 3 through 14 or resid 16...
22(chain C and (resid 3 through 14 or resid 16...
32(chain D and (resid 3 through 14 or resid 16...
42(chain F and (resid 3 through 14 or resid 16...
52(chain G and (resid 3 through 14 or resid 16...
62(chain H and (resid 3 through 14 or resid 16...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 92 or resid 94...A2 - 92
121(chain A and (resid 2 through 92 or resid 94...A94 - 127
131(chain A and (resid 2 through 92 or resid 94...A2 - 1236
141(chain A and (resid 2 through 92 or resid 94...A1034 - 1234
151(chain A and (resid 2 through 92 or resid 94...A1301 - 1303
211(chain E and (resid 2 through 92 or resid 94...E2 - 92
221(chain E and (resid 2 through 92 or resid 94...E94 - 127
231(chain E and (resid 2 through 92 or resid 94...E129 - 1032
241(chain E and (resid 2 through 92 or resid 94...E1034 - 1234
251(chain E and (resid 2 through 92 or resid 94...E1301 - 1303
112(chain B and (resid 3 through 14 or resid 16...B3 - 14
122(chain B and (resid 3 through 14 or resid 16...B16 - 25
132(chain B and (resid 3 through 14 or resid 16...B27 - 85
142(chain B and (resid 3 through 14 or resid 16...B87 - 112
152(chain B and (resid 3 through 14 or resid 16...B122 - 127
162(chain B and (resid 3 through 14 or resid 16...B129
172(chain B and (resid 3 through 14 or resid 16...B131 - 140
182(chain B and (resid 3 through 14 or resid 16...B142 - 144
192(chain B and (resid 3 through 14 or resid 16...B151 - 155
1102(chain B and (resid 3 through 14 or resid 16...B207
1112(chain B and (resid 3 through 14 or resid 16...B207
1122(chain B and (resid 3 through 14 or resid 16...B209 - 225
1132(chain B and (resid 3 through 14 or resid 16...B228 - 258
1142(chain B and (resid 3 through 14 or resid 16...B260 - 264
1152(chain B and (resid 3 through 14 or resid 16...B267 - 273
1162(chain B and (resid 3 through 14 or resid 16...B276 - 2844
1172(chain B and (resid 3 through 14 or resid 16...B346 - 354
1182(chain B and (resid 3 through 14 or resid 16...B356354
1192(chain B and (resid 3 through 14 or resid 16...B356 - 367
1202(chain B and (resid 3 through 14 or resid 16...B371 - 1015
1212(chain B and (resid 3 through 14 or resid 16...B1018 - 1025
1222(chain B and (resid 3 through 14 or resid 16...B1029
1232(chain B and (resid 3 through 14 or resid 16...B1031 - 16
1242(chain B and (resid 3 through 14 or resid 16...B1045 - 1048
1252(chain B and (resid 3 through 14 or resid 16...B2 - 1236
1262(chain B and (resid 3 through 14 or resid 16...B1050 - 1072
1272(chain B and (resid 3 through 14 or resid 16...B1074
1282(chain B and (resid 3 through 14 or resid 16...B1078
1292(chain B and (resid 3 through 14 or resid 16...B1081 - 1093
1302(chain B and (resid 3 through 14 or resid 16...B1095 - 1101144
1312(chain B and (resid 3 through 14 or resid 16...B1146 - 1153
1322(chain B and (resid 3 through 14 or resid 16...B46 - 1153
1332(chain B and (resid 3 through 14 or resid 16...B1155 - 1162
1342(chain B and (resid 3 through 14 or resid 16...B1164 - 1206
1352(chain B and (resid 3 through 14 or resid 16...B1208 - 1231
1362(chain B and (resid 3 through 14 or resid 16...B1234
1372(chain B and (resid 3 through 14 or resid 16...B1303 - 1304
212(chain C and (resid 3 through 14 or resid 16...C3 - 14
222(chain C and (resid 3 through 14 or resid 16...C16 - 25
232(chain C and (resid 3 through 14 or resid 16...C27 - 85
242(chain C and (resid 3 through 14 or resid 16...C2 - 1236
252(chain C and (resid 3 through 14 or resid 16...C129
262(chain C and (resid 3 through 14 or resid 16...C2 - 1236
272(chain C and (resid 3 through 14 or resid 16...C2 - 1236
282(chain C and (resid 3 through 14 or resid 16...C4
292(chain C and (resid 3 through 14 or resid 16...C151 - 155
2102(chain C and (resid 3 through 14 or resid 16...C20
2112(chain C and (resid 3 through 14 or resid 16...C209 - 225
2122(chain C and (resid 3 through 14 or resid 16...C228 - 258
2132(chain C and (resid 3 through 14 or resid 16...C0
2142(chain C and (resid 3 through 14 or resid 16...C29
2152(chain C and (resid 3 through 14 or resid 16...C4
2162(chain C and (resid 3 through 14 or resid 16...C371 - 1015
2172(chain C and (resid 3 through 14 or resid 16...C1018 - 102
2182(chain C and (resid 3 through 14 or resid 16...C102029
2192(chain C and (resid 3 through 14 or resid 16...C1031 - 1032
2202(chain C and (resid 3 through 14 or resid 16...C10
2212(chain C and (resid 3 through 14 or resid 16...C1045 - 1048
2222(chain C and (resid 3 through 14 or resid 16...C1050 - 10
2232(chain C and (resid 3 through 14 or resid 16...C10
2242(chain C and (resid 3 through 14 or resid 16...C1095
2252(chain C and (resid 3 through 14 or resid 16...C1107 - 1144
2262(chain C and (resid 3 through 14 or resid 16...C0
2272(chain C and (resid 3 through 14 or resid 16...C1164 - 1206
2282(chain C and (resid 3 through 14 or resid 16...C1208 - 1231
2292(chain C and (resid 3 through 14 or resid 16...C1234
2302(chain C and (resid 3 through 14 or resid 16...C1303 - 1304
312(chain D and (resid 3 through 14 or resid 16...D3 - 14
322(chain D and (resid 3 through 14 or resid 16...D16 - 25
332(chain D and (resid 3 through 14 or resid 16...D27 - 85
342(chain D and (resid 3 through 14 or resid 16...D2 - 1236
352(chain D and (resid 3 through 14 or resid 16...D129
362(chain D and (resid 3 through 14 or resid 16...D2 - 1236
372(chain D and (resid 3 through 14 or resid 16...D2 - 1236
382(chain D and (resid 3 through 14 or resid 16...D5
392(chain D and (resid 3 through 14 or resid 16...D157 - 163
3102(chain D and (resid 3 through 14 or resid 16...D26
3112(chain D and (resid 3 through 14 or resid 16...D276 - 288
3122(chain D and (resid 3 through 14 or resid 16...D290 - 344
3132(chain D and (resid 3 through 14 or resid 16...D371
3142(chain D and (resid 3 through 14 or resid 16...D2 - 1236
3152(chain D and (resid 3 through 14 or resid 16...D1029
3162(chain D and (resid 3 through 14 or resid 16...D2 - 1236
3172(chain D and (resid 3 through 14 or resid 16...D1036
3182(chain D and (resid 3 through 14 or resid 16...D2 - 1236
3192(chain D and (resid 3 through 14 or resid 16...D1050 - 10
3202(chain D and (resid 3 through 14 or resid 16...D2 - 1236
3212(chain D and (resid 3 through 14 or resid 16...D1081 - 1093
3222(chain D and (resid 3 through 14 or resid 16...D1081 - 1093
3232(chain D and (resid 3 through 14 or resid 16...D1095
3242(chain D and (resid 3 through 14 or resid 16...D1146 - 1153
3252(chain D and (resid 3 through 14 or resid 16...D1155 - 1162
3262(chain D and (resid 3 through 14 or resid 16...D1164 - 1206
3272(chain D and (resid 3 through 14 or resid 16...D1208 - 1231
3282(chain D and (resid 3 through 14 or resid 16...D1208 - 1231
3292(chain D and (resid 3 through 14 or resid 16...D1234
3302(chain D and (resid 3 through 14 or resid 16...D1303 - 1304
412(chain F and (resid 3 through 14 or resid 16...F3 - 14
422(chain F and (resid 3 through 14 or resid 16...F16 - 25
432(chain F and (resid 3 through 14 or resid 16...F27 - 85
442(chain F and (resid 3 through 14 or resid 16...F122 - 127
452(chain F and (resid 3 through 14 or resid 16...F129
462(chain F and (resid 3 through 14 or resid 16...F131 - 140
472(chain F and (resid 3 through 14 or resid 16...F142 - 144
482(chain F and (resid 3 through 14 or resid 16...F151 - 155
492(chain F and (resid 3 through 14 or resid 16...F157 - 163
4102(chain F and (resid 3 through 14 or resid 16...F178 - 199
4112(chain F and (resid 3 through 14 or resid 16...F207
4122(chain F and (resid 3 through 14 or resid 16...F209 - 225
4132(chain F and (resid 3 through 14 or resid 16...F228 - 258
4142(chain F and (resid 3 through 14 or resid 16...F260 - 264
4152(chain F and (resid 3 through 14 or resid 16...F267 - 273
4162(chain F and (resid 3 through 14 or resid 16...F276 - 288
4172(chain F and (resid 3 through 14 or resid 16...F290 - 344
4182(chain F and (resid 3 through 14 or resid 16...F346 - 354
4192(chain F and (resid 3 through 14 or resid 16...F356 - 367
4202(chain F and (resid 3 through 14 or resid 16...F371 - 1015
4212(chain F and (resid 3 through 14 or resid 16...F1018 - 1025
4222(chain F and (resid 3 through 14 or resid 16...F1029
4232(chain F and (resid 3 through 14 or resid 16...F1031 - 1032
4242(chain F and (resid 3 through 14 or resid 16...F1036 - 1042
4252(chain F and (resid 3 through 14 or resid 16...F1045 - 1048
4262(chain F and (resid 3 through 14 or resid 16...F1050 - 1072
4272(chain F and (resid 3 through 14 or resid 16...F1074
4282(chain F and (resid 3 through 14 or resid 16...F1078
4292(chain F and (resid 3 through 14 or resid 16...F1081 - 1093
4302(chain F and (resid 3 through 14 or resid 16...F1095 - 1105
4312(chain F and (resid 3 through 14 or resid 16...F1107 - 1144
4322(chain F and (resid 3 through 14 or resid 16...F1146 - 1153
4332(chain F and (resid 3 through 14 or resid 16...F1155 - 1162
4342(chain F and (resid 3 through 14 or resid 16...F1164 - 1206
4352(chain F and (resid 3 through 14 or resid 16...F1208 - 1231
4362(chain F and (resid 3 through 14 or resid 16...F1234
4372(chain F and (resid 3 through 14 or resid 16...F1303 - 1304
512(chain G and (resid 3 through 14 or resid 16...G3 - 14
522(chain G and (resid 3 through 14 or resid 16...G16 - 25
532(chain G and (resid 3 through 14 or resid 16...G27 - 85
542(chain G and (resid 3 through 14 or resid 16...G122 - 127
552(chain G and (resid 3 through 14 or resid 16...G129
562(chain G and (resid 3 through 14 or resid 16...G131 - 140
572(chain G and (resid 3 through 14 or resid 16...G142 - 144
582(chain G and (resid 3 through 14 or resid 16...G151 - 155
592(chain G and (resid 3 through 14 or resid 16...G157 - 163
5102(chain G and (resid 3 through 14 or resid 16...G178 - 199
5112(chain G and (resid 3 through 14 or resid 16...G207
5122(chain G and (resid 3 through 14 or resid 16...G209 - 225
5132(chain G and (resid 3 through 14 or resid 16...G228 - 258
5142(chain G and (resid 3 through 14 or resid 16...G260 - 264
5152(chain G and (resid 3 through 14 or resid 16...G267 - 273
5162(chain G and (resid 3 through 14 or resid 16...G276 - 288
5172(chain G and (resid 3 through 14 or resid 16...G290 - 344
5182(chain G and (resid 3 through 14 or resid 16...G346 - 354
5192(chain G and (resid 3 through 14 or resid 16...G356 - 367
5202(chain G and (resid 3 through 14 or resid 16...G371 - 1015
5212(chain G and (resid 3 through 14 or resid 16...G1018 - 1025
5222(chain G and (resid 3 through 14 or resid 16...G1029
5232(chain G and (resid 3 through 14 or resid 16...G1031 - 1032
5242(chain G and (resid 3 through 14 or resid 16...G1036 - 1042
5252(chain G and (resid 3 through 14 or resid 16...G1045 - 1048
5262(chain G and (resid 3 through 14 or resid 16...G1050 - 1072
5272(chain G and (resid 3 through 14 or resid 16...G1074
5282(chain G and (resid 3 through 14 or resid 16...G1078
5292(chain G and (resid 3 through 14 or resid 16...G1081 - 1093
5302(chain G and (resid 3 through 14 or resid 16...G1095 - 1105
5312(chain G and (resid 3 through 14 or resid 16...G1107 - 1144
5322(chain G and (resid 3 through 14 or resid 16...G1146 - 1153
5332(chain G and (resid 3 through 14 or resid 16...G1155 - 1162
5342(chain G and (resid 3 through 14 or resid 16...G1164 - 1206
5352(chain G and (resid 3 through 14 or resid 16...G1208 - 1231
5362(chain G and (resid 3 through 14 or resid 16...G1234
5372(chain G and (resid 3 through 14 or resid 16...G1303 - 1304
612(chain H and (resid 3 through 14 or resid 16...H3 - 14
622(chain H and (resid 3 through 14 or resid 16...H16 - 25
632(chain H and (resid 3 through 14 or resid 16...H2 - 1236
642(chain H and (resid 3 through 14 or resid 16...H87 - 127
652(chain H and (resid 3 through 14 or resid 16...H129
662(chain H and (resid 3 through 14 or resid 16...H131 - 140
672(chain H and (resid 3 through 14 or resid 16...H142 - 155
682(chain H and (resid 3 through 14 or resid 16...H157 - 207
692(chain H and (resid 3 through 14 or resid 16...H209 - 258
6102(chain H and (resid 3 through 14 or resid 16...H29 - 258
6112(chain H and (resid 3 through 14 or resid 16...H260 - 273
6122(chain H and (resid 3 through 14 or resid 16...H276 - 288
6132(chain H and (resid 3 through 14 or resid 16...H290 - 344
6142(chain H and (resid 3 through 14 or resid 16...H346 - 354
6152(chain H and (resid 3 through 14 or resid 16...H356 - 36015
6162(chain H and (resid 3 through 14 or resid 16...H1018 - 1025
6172(chain H and (resid 3 through 14 or resid 16...H8 - 1025
6182(chain H and (resid 3 through 14 or resid 16...H1029
6192(chain H and (resid 3 through 14 or resid 16...H1031 - 1032
6202(chain H and (resid 3 through 14 or resid 16...H1036 - 1042
6212(chain H and (resid 3 through 14 or resid 16...H1045 - 1048
6222(chain H and (resid 3 through 14 or resid 16...H1051074
6232(chain H and (resid 3 through 14 or resid 16...H1078
6242(chain H and (resid 3 through 14 or resid 16...H108178
6252(chain H and (resid 3 through 14 or resid 16...H1081 - 1093
6262(chain H and (resid 3 through 14 or resid 16...H1095 - 1105
6272(chain H and (resid 3 through 14 or resid 16...H1107 - 1144
6282(chain H and (resid 3 through 14 or resid 16...H1146 - 1153
6292(chain H and (resid 3 through 14 or resid 16...H2 - 1236
6302(chain H and (resid 3 through 14 or resid 16...H1208 - 123
6312(chain H and (resid 3 through 14 or resid 16...H1234
6322(chain H and (resid 3 through 14 or resid 16...H1303 - 1304

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera / Apolipoprotein B mRNA-editing enzyme 1 / HEPR / mRNA(cytosine(6666)) deaminase 1


分子量: 67073.312 Da / 分子数: 8
変異: A338V,M46A,R48S,E63A,M80T,W121M,A146D,L173A,W199A,F205A
由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (大腸菌), (組換発現) Homo sapiens (ヒト)
遺伝子: DAH37_23060, APOBEC1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A4Z0THX4, UniProt: P41238, UniProt: P0AEX9*PLUS, mRNA(cytosine6666) deaminase
#2: 多糖
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


タイプ: oligosaccharide, Oligosaccharide / クラス: 栄養素 / 分子量: 342.297 Da / 分子数: 14 / 由来タイプ: 組換発現 / 詳細: oligosaccharide / 参照: alpha-maltose
記述子タイププログラム
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / ジメチルアルシン酸アニオン


分子量: 136.989 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C2H6AsO2
研究の焦点であるリガンドがあるかY

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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: 3.13 Å3/Da / 溶媒含有率: 60.72 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6
詳細: 0.2 M potassium chloride, 0.2 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate, pH 6.0, 8.5% PEG8000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 5.0.2 / 波長: 1.28345 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年12月17日
放射モノクロメーター: double crystal Si(111) / 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: 1.28345 Å / 相対比: 1
反射解像度: 3.5→50 Å / Num. obs: 83654 / % possible obs: 99.2 % / 冗長度: 4.9 % / CC1/2: 0.883 / Net I/σ(I): 5.22
反射 シェル解像度: 3.5→3.56 Å / 冗長度: 3.7 % / Rmerge(I) obs: 1.15 / Num. unique obs: 4100 / CC1/2: 0.213 / CC star: 0.593 / % possible all: 98.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18_3845精密化
HKL-2000データスケーリング
PDB_EXTRACT3.25データ抽出
HKL-2000データ削減
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 1ANF & 2NYT

1anf

2nyt


解像度: 3.51→49.61 Å / SU ML: 0.65 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 33.17 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.298 8334 9.99 %
Rwork0.2762 75124 -
obs0.2784 83458 98.52 %
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 max: 295.45 Å2 / Biso mean: 136.6014 Å2 / Biso min: 40.72 Å2
精密化ステップサイクル: final / 解像度: 3.51→49.61 Å
タンパク質核酸リガンド溶媒全体
原子数37254 0 370 0 37624
Biso mean--142.5 --
残基数----4667
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3540X-RAY DIFFRACTION7.049TORSIONAL
12E3540X-RAY DIFFRACTION7.049TORSIONAL
21B8514X-RAY DIFFRACTION7.049TORSIONAL
22C8514X-RAY DIFFRACTION7.049TORSIONAL
23D8514X-RAY DIFFRACTION7.049TORSIONAL
24F8514X-RAY DIFFRACTION7.049TORSIONAL
25G8514X-RAY DIFFRACTION7.049TORSIONAL
26H8514X-RAY DIFFRACTION7.049TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.51-3.550.42432170.45652060227782
3.55-3.590.46582710.44312470274198
3.59-3.630.47512740.45532480275498
3.63-3.680.58212670.60792415268297
3.68-3.730.53982780.46592450272897
3.73-3.780.38852820.39522499278199
3.78-3.830.42522670.39262464273199
3.83-3.890.5012750.50712436271197
3.89-3.950.5462680.54142412268095
3.95-4.010.3922650.34022489275499
4.01-4.080.30882720.31652485275799
4.08-4.160.33772800.31022514279499
4.16-4.240.30732800.29732507278799
4.24-4.320.3182800.28512514279499
4.32-4.420.31322800.274225032783100
4.42-4.520.29042810.258825292810100
4.52-4.630.27682800.24324932773100
4.63-4.760.27122840.230725612845100
4.76-4.90.23512810.220824982779100
4.9-5.060.24032820.22225432825100
5.06-5.240.25462820.217925342816100
5.24-5.450.25312820.236325452827100
5.45-5.690.26242900.231625302820100
5.69-5.990.26562790.247325592838100
5.99-6.370.23332810.225625732854100
6.37-6.860.24752850.22625552840100
6.86-7.550.24182830.224325782861100
7.55-8.630.21512880.194925932881100
8.64-10.860.22870.166926092896100
10.86-49.610.263130.22982726303999
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)
11.7032-0.9827-0.77712.03851.31131.7507-0.06-0.3809-0.06630.03260.0877-0.30930.19490.3572-0.13070.73530.190.00211.2571-0.17661.2035-25.4868-30.9651-98.7993
20.95590.44350.57030.9078-0.28081.0972-0.29350.7542-1.0956-0.4736-0.3394-1.0567-0.05430.224-0.71620.2984-0.0485-0.01861.4987-0.53852.1815-8.956-9.8273-77.938
31.2177-1.61410.86582.6623-0.66463.7881-0.118-0.0079-0.57520.52320.1304-1.2184-0.30740.08620.1420.5362-0.0493-0.03811.1277-0.28951.396-21.40167.8405-68.4305
44.451.48271.35145.31121.13064.24010.06850.14930.318-0.5573-0.1311-0.85890.5290.29730.25430.7211-0.0168-0.21060.61850.09211.0744-13.168439.6979-61.3182
52.18930.96070.73154.4416-0.23812.4286-0.54530.35242.0752-0.2622-0.26080.4772-1.12930.07180.42361.0843-0.1168-0.43220.73780.44641.8632-15.667560.2112-67.7135
64.4310.1021.13123.47311.96453.32510.09990.63871.7501-1.21390.33731.3673-1.0989-0.30620.64590.8276-0.2055-0.36411.44860.31271.1247-33.25337.2887-82.3006
74.06231.97080.58034.17191.13984.41720.14290.21650.8399-0.9530.00122.0914-1.0015-0.17020.90990.8339-0.0047-0.41211.38010.00221.1633-44.881430.796-82.3249
81.84181.04471.28286.9998-0.15741.1095-0.31131.64750.1549-1.5975-0.6085-1.7623-0.01570.4098-0.26870.72720.39820.14631.64050.53671.0165-25.783127.8515-88.1657
95.1450.8051.93252.30480.66091.6997-0.34760.3123-0.6888-0.5892-0.45580.90330.30250.0816-0.50440.1454-0.186-0.4281.2003-0.57860.8662-35.86849.9879-77.0667
104.93830.60410.22852.99180.59192.19270.27420.0489-0.3636-0.17740.0639-0.0352-0.24620.4725-0.10950.3916-0.0924-0.13030.9657-0.3340.8951-91.7263-18.5852-85.5769
114.42330.4799-0.01012.6768-1.16122.00640.4723-0.6468-0.55720.269-0.22920.83130.3092-0.1255-0.14490.6896-0.1745-0.16030.79310.00080.78-91.0863-33.4991-70.427
123.99271.8128-0.67171.72710.55312.86790.3467-0.1718-0.24690.4857-0.13390.19950.1020.3201-0.05460.48360.0613-0.10341.0347-0.11591.2296-64.6039-15.7004-75.6477
134.48010.4398-0.11232.9852-1.04512.92630.02290.15780.01630.0396-0.1627-0.371-0.14510.56910.00750.35720.08490.07341.1028-0.26650.7246-58.5219-3.3275-84.2076
142.9826-0.856-0.46121.8471-0.63631.7437-0.7086-0.06090.54530.11461.4456-0.7833-1.20631.9497-0.01621.471-0.42630.51712.2938-0.0272.5609-32.600616.807-112.3217
154.58910.6637-0.54181.1615-1.5091.99050.45220.89132.1001-0.4362-0.405-0.60030.32391.4786-0.07541.5496-0.15290.52722.7940.24572.0488-24.16218.6221-130.7338
162.1262-0.8283-1.49972.84291.42571.2195-0.04820.80110.7543-2.0112-0.44630.0373-0.3693-0.2776-0.08871.348-0.11910.37542.46550.13831.1105-48.50881.0833-131.1866
173.51240.725-0.14513.00690.42754.19970.46681.00550.5673-0.9983-0.1319-0.31970.1117-0.2101-0.03460.8160.1035-0.20561.3669-0.06910.4172-64.32970.1205-117.0751
182.28-0.86811.09091.4023-0.581.77220.219-0.0145-0.3348-0.4975-0.12660.14180.45140.1633-0.14171.40920.2005-0.25190.72620.02841.190330.9225.8375-6.4951
191.5279-0.1328-0.3311.86230.43981.96180.16840.3514-1.01520.96050.1427-0.85790.2536-0.3320.41341.5147-0.1917-0.62320.0622-0.10632.23364.28613.081-30.443
205.04691.5403-0.08483.45260.37323.4219-0.2682-0.30670.10290.6712-0.19021.26820.0761-0.7620.37310.7091-0.030.19830.8506-0.23121.4857-55.414415.3135-39.1004
213.01210.7751.91163.83611.69661.89530.9805-1.38511.12710.0857-0.48961.4225-0.4845-0.3660.68561.4681-0.32380.22010.8428-0.37020.3897-37.144533.5998-23.1692
225.2331.17410.42844.76730.64872.4636-0.3979-0.87530.51850.4062-0.08910.51750.2396-0.5450.33751.23860.0001-0.08660.9224-0.37120.8978-29.536638.2757-21.0458
234.22961.21050.92594.54712.10351.4725-0.1721-0.04990.91320.0142-0.2214-0.3915-0.3609-0.0435-0.12071.2803-0.0643-0.38120.3099-0.33220.4773-9.81736.104-28.3763
243.4388-0.0201-0.87783.82610.53451.6279-0.08770.230.8397-0.06250.4049-0.359-0.0590.2755-0.15410.8964-0.1364-0.14210.5551-0.05170.549628.761393.491-29.9701
251.73390.9445-0.97413.53050.24061.5399-0.31390.0159-0.2709-0.61520.2606-0.54340.21780.419-0.12970.9078-0.19050.12780.8879-0.44771.328429.857778.8441-33.7292
262.28251.10620.67495.1302-1.27412.7626-0.51710.7925-0.0971-0.52430.22370.65820.52660.4042-0.16941.0870-0.3120.6626-0.10520.730913.657263.357-32.3817
273.00860.1410.05874.16150.15942.1235-0.212-0.0496-0.26440.29740.03360.16130.3816-0.0884-0.13641.09420.0756-0.25680.27760.03640.63273.065359.0279-20.6023
283.2566-0.47740.36641.732-0.24872.56030.61650.221-0.80270.5423-0.4781.61161.3988-0.5080.16462.1927-0.22660.15051.23260.49383.1903-19.309233.69478.828
291.16490.6785-1.08434.6470.01141.5089-0.4733-1.2466-0.350.92510.09791.8231.6361-0.1045-0.0942.9765-0.09720.19711.18240.67011.9344-14.114128.015125.2157
302.5820.3207-0.70833.38180.43631.91450.1548-1.5686-0.91271.3208-0.4834-0.41470.13040.13020.04262.10170.0994-0.02212.11960.06531.0938-3.003560.3428.5938
313.40890.93271.06423.53190.39654.086-0.0187-1.0169-0.40340.24660.31460.2235-0.26170.02130.0251.33730.1943-0.16770.8108-0.14750.51850.562264.94967.9872
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 1038 )A2 - 1038
2X-RAY DIFFRACTION2chain 'A' and (resid 1039 through 1172 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1173 through 1236 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 83 )B2 - 83
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 369 )B84 - 369
6X-RAY DIFFRACTION6chain 'B' and (resid 370 through 1072 )B370 - 1072
7X-RAY DIFFRACTION7chain 'B' and (resid 1073 through 1136 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1137 through 1171 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1172 through 1236 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 97 )C2 - 97
11X-RAY DIFFRACTION11chain 'C' and (resid 98 through 366 )C98 - 366
12X-RAY DIFFRACTION12chain 'C' and (resid 367 through 1072 )C367 - 1072
13X-RAY DIFFRACTION13chain 'C' and (resid 1073 through 1236 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 83 )D2 - 83
15X-RAY DIFFRACTION15chain 'D' and (resid 84 through 352 )D84 - 352
16X-RAY DIFFRACTION16chain 'D' and (resid 353 through 1075 )D353 - 1075
17X-RAY DIFFRACTION17chain 'D' and (resid 1076 through 1236 )D0
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 1038 )E2 - 1038
19X-RAY DIFFRACTION19chain 'E' and (resid 1039 through 1236 )E0
20X-RAY DIFFRACTION20chain 'F' and (resid 2 through 369 )F2 - 369
21X-RAY DIFFRACTION21chain 'F' and (resid 370 through 1072 )F370 - 1072
22X-RAY DIFFRACTION22chain 'F' and (resid 1073 through 1171 )F0
23X-RAY DIFFRACTION23chain 'F' and (resid 1172 through 1236 )F0
24X-RAY DIFFRACTION24chain 'G' and (resid 2 through 315 )G2 - 315
25X-RAY DIFFRACTION25chain 'G' and (resid 316 through 1026 )G316 - 1026
26X-RAY DIFFRACTION26chain 'G' and (resid 1027 through 1075 )G0
27X-RAY DIFFRACTION27chain 'G' and (resid 1076 through 1236 )G0
28X-RAY DIFFRACTION28chain 'H' and (resid 2 through 97 )H2 - 97
29X-RAY DIFFRACTION29chain 'H' and (resid 98 through 1044 )H98 - 1044
30X-RAY DIFFRACTION30chain 'H' and (resid 1045 through 1106 )H0
31X-RAY DIFFRACTION31chain 'H' and (resid 1107 through 1236 )H0

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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。
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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

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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

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