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- PDB-5nue: Cytosolic Malate Dehydrogenase 1 (peroxide-treated) -

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基本情報

登録情報
データベース: PDB / ID: 5nue
タイトルCytosolic Malate Dehydrogenase 1 (peroxide-treated)
要素(Malate dehydrogenase 1, ...) x 3
キーワードOXIDOREDUCTASE / Dehydrogenase / Oxidized / Malate/Oxaloacetate / NAD+
機能・相同性
機能・相同性情報


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / apoplast / plasmodesma / plant-type vacuole / chloroplast stroma / response to zinc ion / tricarboxylic acid cycle / chloroplast ...malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / apoplast / plasmodesma / plant-type vacuole / chloroplast stroma / response to zinc ion / tricarboxylic acid cycle / chloroplast / mRNA binding / extracellular region / nucleus / plasma membrane / cytosol
類似検索 - 分子機能
Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain ...Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
ACETATE ION / 2-ETHOXYETHANOL / FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / HYDROGEN PEROXIDE / Malate dehydrogenase 1, cytoplasmic
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: 1.35000279615 Å
データ登録者Young, D. / Messens, J. / Huang, J. / Reichheld, J.-P.
資金援助 フランス, ベルギー, 4件
組織認可番号国
Centre National de la Recherche Scientifique and the Agence Nationale de la RechercheANR-Blanc Cynthiol 12-BSV6-0011 フランス
VIB ベルギー
Vrije Universiteit BrusselSPR34 ベルギー
Research Foundation - Flanders (FWO) ベルギー
引用ジャーナル: J. Exp. Bot. / 年: 2018
タイトル: Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis.
著者: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / ...著者: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / Messens, J. / Reichheld, J.P.
履歴
登録2017年4月29日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年2月28日Provider: repository / タイプ: Initial release
改定 1.12018年7月4日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.22025年4月9日Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Malate dehydrogenase 1, cytoplasmic
B: Malate dehydrogenase 1, cytoplasmic
C: Malate dehydrogenase 1, cytoplasmic
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)111,42044
ポリマ－106,9293
非ポリマー4,49141
水17,997999
1
A: Malate dehydrogenase 1, cytoplasmic
B: Malate dehydrogenase 1, cytoplasmic
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)74,44331
ポリマ－71,2862
非ポリマー3,15729
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-103 kcal/mol
Surface area24100 Å2
手法PISA
2
C: Malate dehydrogenase 1, cytoplasmic
ヘテロ分子

C: Malate dehydrogenase 1, cytoplasmic
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)73,95426
ポリマ－71,2862
非ポリマー2,66824
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area10220 Å2
ΔGint-110 kcal/mol
Surface area24750 Å2
手法PISA
単位格子
Length a, b, c (Å)64.598, 118.374, 148.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDモデル要素
11C-797-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYS(chain 'A' and (resid 2 through 3 or resid 6...AA2 - 32 - 3
12VALVALALAALA(chain 'A' and (resid 2 through 3 or resid 6...AA6 - 146 - 14
13ILEILEPROPRO(chain 'A' and (resid 2 through 3 or resid 6...AA17 - 2317 - 23
14ILEILEILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA2525
15METMETGLYGLY(chain 'A' and (resid 2 through 3 or resid 6...AA30 - 3230 - 32
16GLNGLNHISHIS(chain 'A' and (resid 2 through 3 or resid 6...AA35 - 4035 - 40
17LEULEUALAALA(chain 'A' and (resid 2 through 3 or resid 6...AA42 - 4742 - 47
18ALAALALEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA50 - 5150 - 51
19GLYGLYLYSLYS(chain 'A' and (resid 2 through 3 or resid 6...AA53 - 5553 - 55
110GLUGLULEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA57 - 5857 - 58
111ASPASPVALVAL(chain 'A' and (resid 2 through 3 or resid 6...AA60 - 8660 - 86
112VALVALARGARG(chain 'A' and (resid 2 through 3 or resid 6...AA88 - 9388 - 93
113GLUGLUGLUGLU(chain 'A' and (resid 2 through 3 or resid 6...AA9595
114GLUGLUVALVAL(chain 'A' and (resid 2 through 3 or resid 6...AA98 - 10298 - 102
115LYSLYSVALVAL(chain 'A' and (resid 2 through 3 or resid 6...AA105 - 107105 - 107
116ILEILELEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA109 - 117109 - 117
117HISHISALAALA(chain 'A' and (resid 2 through 3 or resid 6...AA120 - 121120 - 121
118CYSCYSCYSCYS(chain 'A' and (resid 2 through 3 or resid 6...AA125125
119VALVALASNASN(chain 'A' and (resid 2 through 3 or resid 6...AA127 - 132127 - 132
120ALAALAILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA134 - 140134 - 140
121GLUGLUPROPRO(chain 'A' and (resid 2 through 3 or resid 6...AA143 - 146143 - 146
122ILEILEPROPRO(chain 'A' and (resid 2 through 3 or resid 6...AA148 - 149148 - 149
123ASNASNGLNGLN(chain 'A' and (resid 2 through 3 or resid 6...AA152 - 167152 - 167
124GLUGLUSERSER(chain 'A' and (resid 2 through 3 or resid 6...AA170 - 189170 - 189
125SERSERASNASN(chain 'A' and (resid 2 through 3 or resid 6...AA191 - 197191 - 197
126ALAALALYSLYS(chain 'A' and (resid 2 through 3 or resid 6...AA199 - 208199 - 208
127VALVALASPASP(chain 'A' and (resid 2 through 3 or resid 6...AA210 - 221210 - 221
128PHEPHEILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA224 - 225224 - 225
129THRTHRILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA227 - 235227 - 235
130LYSLYSARGARG(chain 'A' and (resid 2 through 3 or resid 6...AA237 - 239237 - 239
131SERSERALAALA(chain 'A' and (resid 2 through 3 or resid 6...AA246 - 247246 - 247
132ALAALAILEILE(chain 'A' and (resid 2 through 3 or resid 6...AA251 - 255251 - 255
133ASPASPTYRTYR(chain 'A' and (resid 2 through 3 or resid 6...AA257 - 273257 - 273
134ASPASPPROPRO(chain 'A' and (resid 2 through 3 or resid 6...AA275 - 281275 - 281
135GLYGLYASNASN(chain 'A' and (resid 2 through 3 or resid 6...AA283 - 294283 - 294
136TRPTRPTRPTRP(chain 'A' and (resid 2 through 3 or resid 6...AA297297
137ILEILEASPASP(chain 'A' and (resid 2 through 3 or resid 6...AA299 - 306299 - 306
138VALVALARGARG(chain 'A' and (resid 2 through 3 or resid 6...AA308 - 310308 - 310
139LYSLYSTHRTHR(chain 'A' and (resid 2 through 3 or resid 6...AA312 - 316312 - 316
140GLUGLULEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA319 - 320319 - 320
141GLUGLULYSLYS(chain 'A' and (resid 2 through 3 or resid 6...AA323 - 324323 - 324
142LEULEULEULEU(chain 'A' and (resid 2 through 3 or resid 6...AA326326
143SERSERSERSER(chain 'A' and (resid 2 through 3 or resid 6...AA332332
244ALAALALYSLYS(chain 'B' and (resid 2 through 3 or resid 6...BB2 - 32 - 3
245VALVALALAALA(chain 'B' and (resid 2 through 3 or resid 6...BB6 - 146 - 14
246ILEILEPROPRO(chain 'B' and (resid 2 through 3 or resid 6...BB17 - 2317 - 23
247ILEILEILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB2525
248METMETGLYGLY(chain 'B' and (resid 2 through 3 or resid 6...BB30 - 3230 - 32
249GLNGLNHISHIS(chain 'B' and (resid 2 through 3 or resid 6...BB35 - 4035 - 40
250LEULEUALAALA(chain 'B' and (resid 2 through 3 or resid 6...BB42 - 4742 - 47
251ALAALALEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB50 - 5150 - 51
252GLYGLYLYSLYS(chain 'B' and (resid 2 through 3 or resid 6...BB53 - 5553 - 55
253GLUGLULEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB57 - 5857 - 58
254ASPASPVALVAL(chain 'B' and (resid 2 through 3 or resid 6...BB60 - 8660 - 86
255VALVALARGARG(chain 'B' and (resid 2 through 3 or resid 6...BB88 - 9388 - 93
256GLUGLUGLUGLU(chain 'B' and (resid 2 through 3 or resid 6...BB9595
257GLUGLUVALVAL(chain 'B' and (resid 2 through 3 or resid 6...BB98 - 10298 - 102
258LYSLYSVALVAL(chain 'B' and (resid 2 through 3 or resid 6...BB105 - 107105 - 107
259ILEILELEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB109 - 117109 - 117
260HISHISALAALA(chain 'B' and (resid 2 through 3 or resid 6...BB120 - 121120 - 121
261CYSCYSCYSCYS(chain 'B' and (resid 2 through 3 or resid 6...BB125125
262VALVALASNASN(chain 'B' and (resid 2 through 3 or resid 6...BB127 - 132127 - 132
263ALAALAILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB134 - 140134 - 140
264GLUGLUPROPRO(chain 'B' and (resid 2 through 3 or resid 6...BB143 - 146143 - 146
265ILEILEPROPRO(chain 'B' and (resid 2 through 3 or resid 6...BB148 - 149148 - 149
266ASNASNGLNGLN(chain 'B' and (resid 2 through 3 or resid 6...BB152 - 167152 - 167
267GLUGLUSERSER(chain 'B' and (resid 2 through 3 or resid 6...BB170 - 189170 - 189
268SERSERASNASN(chain 'B' and (resid 2 through 3 or resid 6...BB191 - 197191 - 197
269ALAALALYSLYS(chain 'B' and (resid 2 through 3 or resid 6...BB199 - 208199 - 208
270VALVALASPASP(chain 'B' and (resid 2 through 3 or resid 6...BB210 - 221210 - 221
271PHEPHEILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB224 - 225224 - 225
272THRTHRILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB227 - 235227 - 235
273LYSLYSARGARG(chain 'B' and (resid 2 through 3 or resid 6...BB237 - 239237 - 239
274SERSERALAALA(chain 'B' and (resid 2 through 3 or resid 6...BB246 - 247246 - 247
275ALAALAILEILE(chain 'B' and (resid 2 through 3 or resid 6...BB251 - 255251 - 255
276ASPASPTYRTYR(chain 'B' and (resid 2 through 3 or resid 6...BB257 - 273257 - 273
277ASPASPPROPRO(chain 'B' and (resid 2 through 3 or resid 6...BB275 - 281275 - 281
278GLYGLYASNASN(chain 'B' and (resid 2 through 3 or resid 6...BB283 - 294283 - 294
279TRPTRPTRPTRP(chain 'B' and (resid 2 through 3 or resid 6...BB297297
280ILEILEASPASP(chain 'B' and (resid 2 through 3 or resid 6...BB299 - 306299 - 306
281VALVALARGARG(chain 'B' and (resid 2 through 3 or resid 6...BB308 - 310308 - 310
282LYSLYSTHRTHR(chain 'B' and (resid 2 through 3 or resid 6...BB312 - 316312 - 316
283GLUGLULEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB319 - 320319 - 320
284GLUGLULYSLYS(chain 'B' and (resid 2 through 3 or resid 6...BB323 - 324323 - 324
285LEULEULEULEU(chain 'B' and (resid 2 through 3 or resid 6...BB326326
286SERSERSERSER(chain 'B' and (resid 2 through 3 or resid 6...BB332332
387ALAALALYSLYS(chain 'C' and (resid 2 through 3 or resid 6...CC2 - 32 - 3
388VALVALALAALA(chain 'C' and (resid 2 through 3 or resid 6...CC6 - 146 - 14
389ILEILEPROPRO(chain 'C' and (resid 2 through 3 or resid 6...CC17 - 2317 - 23
390ILEILEILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC2525
391METMETGLYGLY(chain 'C' and (resid 2 through 3 or resid 6...CC30 - 3230 - 32
392GLNGLNHISHIS(chain 'C' and (resid 2 through 3 or resid 6...CC35 - 4035 - 40
393LEULEUALAALA(chain 'C' and (resid 2 through 3 or resid 6...CC42 - 4742 - 47
394ALAALALEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC50 - 5150 - 51
395GLYGLYLYSLYS(chain 'C' and (resid 2 through 3 or resid 6...CC53 - 5553 - 55
396GLUGLULEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC57 - 5857 - 58
397ASPASPVALVAL(chain 'C' and (resid 2 through 3 or resid 6...CC60 - 8660 - 86
398VALVALARGARG(chain 'C' and (resid 2 through 3 or resid 6...CC88 - 9388 - 93
399GLUGLUGLUGLU(chain 'C' and (resid 2 through 3 or resid 6...CC9595
3100GLUGLUVALVAL(chain 'C' and (resid 2 through 3 or resid 6...CC98 - 10298 - 102
3101LYSLYSVALVAL(chain 'C' and (resid 2 through 3 or resid 6...CC105 - 107105 - 107
3102ILEILELEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC109 - 117109 - 117
3103HISHISALAALA(chain 'C' and (resid 2 through 3 or resid 6...CC120 - 121120 - 121
3104CYSCYSCYSCYS(chain 'C' and (resid 2 through 3 or resid 6...CC125125
3105VALVALASNASN(chain 'C' and (resid 2 through 3 or resid 6...CC127 - 132127 - 132
3106ALAALAILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC134 - 140134 - 140
3107GLUGLUPROPRO(chain 'C' and (resid 2 through 3 or resid 6...CC143 - 146143 - 146
3108ILEILEPROPRO(chain 'C' and (resid 2 through 3 or resid 6...CC148 - 149148 - 149
3109ASNASNGLNGLN(chain 'C' and (resid 2 through 3 or resid 6...CC152 - 167152 - 167
3110GLUGLUSERSER(chain 'C' and (resid 2 through 3 or resid 6...CC170 - 189170 - 189
3111SERSERASNASN(chain 'C' and (resid 2 through 3 or resid 6...CC191 - 197191 - 197
3112ALAALALYSLYS(chain 'C' and (resid 2 through 3 or resid 6...CC199 - 208199 - 208
3113VALVALASPASP(chain 'C' and (resid 2 through 3 or resid 6...CC210 - 221210 - 221
3114PHEPHEILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC224 - 225224 - 225
3115THRTHRILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC227 - 235227 - 235
3116LYSLYSARGARG(chain 'C' and (resid 2 through 3 or resid 6...CC237 - 239237 - 239
3117SERSERALAALA(chain 'C' and (resid 2 through 3 or resid 6...CC246 - 247246 - 247
3118ALAALAILEILE(chain 'C' and (resid 2 through 3 or resid 6...CC251 - 255251 - 255
3119ASPASPTYRTYR(chain 'C' and (resid 2 through 3 or resid 6...CC257 - 273257 - 273
3120ASPASPPROPRO(chain 'C' and (resid 2 through 3 or resid 6...CC275 - 281275 - 281
3121GLYGLYASNASN(chain 'C' and (resid 2 through 3 or resid 6...CC283 - 294283 - 294
3122TRPTRPTRPTRP(chain 'C' and (resid 2 through 3 or resid 6...CC297297
3123ILEILEASPASP(chain 'C' and (resid 2 through 3 or resid 6...CC299 - 306299 - 306
3124VALVALARGARG(chain 'C' and (resid 2 through 3 or resid 6...CC308 - 310308 - 310
3125LYSLYSTHRTHR(chain 'C' and (resid 2 through 3 or resid 6...CC312 - 316312 - 316
3126GLUGLULEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC319 - 320319 - 320
3127GLUGLULYSLYS(chain 'C' and (resid 2 through 3 or resid 6...CC323 - 324323 - 324
3128LEULEULEULEU(chain 'C' and (resid 2 through 3 or resid 6...CC326326
3129SERSERSERSER(chain 'C' and (resid 2 through 3 or resid 6...CC332332

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要素

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Malate dehydrogenase 1, ... , 3種, 3分子 ABC

#1: タンパク質 Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


分子量: 35610.918 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Residue 56 oxidized to methionine sulfoxide
由来: (組換発現) Arabidopsis thaliana (シロイヌナズナ)
Cell: cytoplasmic / 遺伝子: MDH1, At1g04410, F19P19.13 / プラスミド: pDEST17 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): C41 / 参照: UniProt: P93819, malate dehydrogenase
#2: タンパク質 Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


分子量: 35674.914 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Arabidopsis thaliana (シロイヌナズナ)
遺伝子: MDH1, At1g04410, F19P19.13 / プラスミド: pDEST17 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): C41 / 参照: UniProt: P93819, malate dehydrogenase
#3: タンパク質 Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


分子量: 35642.918 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Arabidopsis thaliana (シロイヌナズナ)
遺伝子: MDH1, At1g04410, F19P19.13 / プラスミド: pDEST17 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): C41 / 参照: UniProt: P93819, malate dehydrogenase

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非ポリマー , 10種, 1040分子

#4: 化合物 ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


分子量: 663.425 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C21H27N7O14P2 / コメント: NAD*YM
#5: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 8 / 由来タイプ: 合成 / 式: SO4
#6: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物
ChemComp-PEO / HYDROGEN PEROXIDE


分子量: 34.015 Da / 分子数: 11 / 由来タイプ: 合成 / 式: H2O2
#8: 化合物
ChemComp-FMT / FORMIC ACID / ギ酸


分子量: 46.025 Da / 分子数: 5 / 由来タイプ: 合成 / 式: CH2O2
#9: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#10: 化合物 ChemComp-ETX / 2-ETHOXYETHANOL / 2-エトキシエタノ-ル


分子量: 90.121 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H10O2
#11: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H3O2
#12: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H6O2
#13: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 999 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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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: 2.66 Å3/Da / 溶媒含有率: 53.87 % / 解説: 100 um x 200 um
結晶化温度: 283 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 / 詳細: 1.5 M ammonium sulfate, 0.1 M Tris-HCl

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データ収集

回折平均測定温度: 100 K / Ambient temp details: liquid nitrogen cryostream
放射光源由来: シンクロトロン / サイト: SOLEIL / ビームライン: PROXIMA 2 / 波長: 0.980105 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2016年2月14日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.980105 Å / 相対比: 1
反射解像度: 1.35→92.561 Å / Num. obs: 236503 / % possible obs: 99.96 % / 冗長度: 13.6 % / Biso Wilson estimate: 14.47098422 Å2 / CC1/2: 0.973 / Rrim(I) all: 0.1092 / Net I/σ(I): 5.56
反射 シェル解像度: 1.35→1.398 Å / 冗長度: 13.4 % / Mean I/σ(I) obs: 0.63 / CC1/2: 0.369 / Rpim(I) all: 0.798 / Rrim(I) all: 2.934 / % possible all: 99.98

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
XDSデータ削減
Aimless0.5.32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 / 解像度: 1.35000279615→92.5612886735 Å / SU ML: 0.163547634761 / 交差検証法: FREE R-VALUE / σ(F): 1.32522207677 / 位相誤差: 19.3646044324
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.179506294341 12401 4.98260247664 %
Rwork0.146297730068 236485 -
obs0.147967919778 248886 99.9213110542 %
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: 21.3464790462 Å2
精密化ステップサイクル: LAST / 解像度: 1.35000279615→92.5612886735 Å
タンパク質核酸リガンド溶媒全体
原子数7454 0 283 999 8736
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01378131529378471
X-RAY DIFFRACTIONf_angle_d1.4132965480611621
X-RAY DIFFRACTIONf_chiral_restr0.1024878580111341
X-RAY DIFFRACTIONf_plane_restr0.008548986203171483
X-RAY DIFFRACTIONf_dihedral_angle_d15.69489762423326
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.3534770925484150.3291972311787742X-RAY DIFFRACTION99.6335654086
1.3653-1.38140.339133700014080.3111337641647777X-RAY DIFFRACTION99.7805680848
1.3814-1.39830.3417938762344120.3046699052527811X-RAY DIFFRACTION99.85428051
1.3983-1.4160.325571749513890.2852612478167826X-RAY DIFFRACTION99.8905642023
1.416-1.43460.3050356264344150.2626751673757872X-RAY DIFFRACTION99.8794745089
1.4346-1.45420.2784718902753900.2602562091797800X-RAY DIFFRACTION99.9633833761
1.4542-1.4750.2851640907243810.2482736482397857X-RAY DIFFRACTION99.9757281553
1.475-1.4970.2758027369814330.2363601775527818X-RAY DIFFRACTION99.9515445185
1.497-1.52040.2515531752233900.2165036185477801X-RAY DIFFRACTION99.9755889174
1.5204-1.54540.2648958041624350.2046022239747852X-RAY DIFFRACTION99.951754915
1.5454-1.5720.2484226737174160.1859796234917813X-RAY DIFFRACTION99.9757016158
1.572-1.60060.2161076683233970.1734826857787819X-RAY DIFFRACTION99.9878301083
1.6006-1.63140.200034286044110.1577038243947841X-RAY DIFFRACTION99.9515503876
1.6314-1.66470.1973767772144290.1462218940467876X-RAY DIFFRACTION99.9879605105
1.6647-1.70090.1747291159474150.1348923662117851X-RAY DIFFRACTION100
1.7009-1.74050.1796108941563810.1360017267827868X-RAY DIFFRACTION100
1.7405-1.7840.1779721533774170.1323359713697814X-RAY DIFFRACTION99.9878522838
1.784-1.83220.1713084797434230.1227106829357876X-RAY DIFFRACTION99.9518246417
1.8322-1.88620.1694879965764290.1265625392667852X-RAY DIFFRACTION99.9879256218
1.8862-1.9470.1717449970824110.1198035490517901X-RAY DIFFRACTION99.9639206254
1.947-2.01660.1719795709834260.1166444075377866X-RAY DIFFRACTION99.9397372544
2.0166-2.09740.1565889588913510.1169523567557918X-RAY DIFFRACTION99.9516499456
2.0974-2.19280.1659888234334200.1177319754427893X-RAY DIFFRACTION99.8798510153
2.1928-2.30850.1524234808864290.1170493241047913X-RAY DIFFRACTION99.8205097523
2.3085-2.45310.1567714613664290.1244260278647891X-RAY DIFFRACTION99.8559769563
2.4531-2.64250.1708446256533910.1292599695317965X-RAY DIFFRACTION99.8446648345
2.6425-2.90850.1622258972684330.1372893544597953X-RAY DIFFRACTION99.9046938289
2.9085-3.32930.1564872556534520.1399840800287957X-RAY DIFFRACTION99.9049542592
3.3293-4.19460.1413581099994460.1236298504628074X-RAY DIFFRACTION99.9882642882
4.1946-92.77960.1657369744234270.1445080789138388X-RAY DIFFRACTION99.9206529132

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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

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  • 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

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