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- PDB-8oje: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 in comp... -

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基本情報

登録情報
データベース: PDB / ID: 8oje
タイトルArabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 in complex with L-malate
要素Phosphoenolpyruvate carboxylase 1
キーワードPLANT PROTEIN / Phosphoenolpyruvate carboxylase / Citric acid cycle / TCA cycle / photosynthesis
機能・相同性
機能・相同性情報


phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / carbon fixation / apoplast / cellular response to phosphate starvation / photosynthesis / tricarboxylic acid cycle / chloroplast / protein tetramerization ...phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / carbon fixation / apoplast / cellular response to phosphate starvation / photosynthesis / tricarboxylic acid cycle / chloroplast / protein tetramerization / nucleus / cytosol
類似検索 - 分子機能
Phosphoenolpyruvate carboxylase, Lys active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase, bacterial/plant-type / Phosphoenolpyruvate carboxylase, His active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase active site 2. / Phosphoenolpyruvate carboxylase active site 1. / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
類似検索 - ドメイン・相同性
(2S)-2-hydroxybutanedioic acid / DI(HYDROXYETHYL)ETHER / Phosphoenolpyruvate carboxylase 1
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: 3.14239899937 Å
データ登録者Haesaerts, S. / Loris, R. / Larsen, P.B.
資金援助 米国, ベルギー, 2件
組織認可番号国
United States Department of Agriculture (USDA)2021-67014-34888 米国
Research Foundation - Flanders (FWO)G011420N ベルギー
引用ジャーナル: To Be Published
タイトル: Amino acid changes that deregulate PHOSPHOENOLPYRUVATE CARBOXYLASE in plants
著者: Meyer, T.J. / Sheng, J. / Haesaerts, S. / Frausto, K. / O'Leary, S. / Loris, R. / Larsen, P.B.
履歴
登録2023年3月24日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年5月31日Provider: repository / タイプ: Initial release
改定 1.12023年11月1日Group: Data collection / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Phosphoenolpyruvate carboxylase 1
B: Phosphoenolpyruvate carboxylase 1
C: Phosphoenolpyruvate carboxylase 1
D: Phosphoenolpyruvate carboxylase 1
E: Phosphoenolpyruvate carboxylase 1
F: Phosphoenolpyruvate carboxylase 1
G: Phosphoenolpyruvate carboxylase 1
H: Phosphoenolpyruvate carboxylase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)897,31879
ポリマ－891,1858
非ポリマー6,13371
水2,396133
1
A: Phosphoenolpyruvate carboxylase 1
B: Phosphoenolpyruvate carboxylase 1
ヘテロ分子

E: Phosphoenolpyruvate carboxylase 1
F: Phosphoenolpyruvate carboxylase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)448,64139
ポリマ－445,5934
非ポリマー3,04935
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
2
C: Phosphoenolpyruvate carboxylase 1
D: Phosphoenolpyruvate carboxylase 1
ヘテロ分子

G: Phosphoenolpyruvate carboxylase 1
H: Phosphoenolpyruvate carboxylase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)448,67740
ポリマ－445,5934
非ポリマー3,08436
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
単位格子
Length a, b, c (Å)116.080, 352.200, 176.040
Angle α, β, γ (deg.)90.000, 101.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81

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
11LEULEULEULEU(chain 'A' and ((resid 6 through 11 and (name N...AA6 - 13913 - 146
12GLUGLUPROPRO(chain 'A' and ((resid 6 through 11 and (name N...AA141 - 154148 - 161
13GLUGLUVALVAL(chain 'A' and ((resid 6 through 11 and (name N...AA156 - 178163 - 185
14ARGARGTHRTHR(chain 'A' and ((resid 6 through 11 and (name N...AA180 - 300187 - 307
15ASPASPGLUGLU(chain 'A' and ((resid 6 through 11 and (name N...AA302 - 320309 - 327
16LEULEUSERSER(chain 'A' and ((resid 6 through 11 and (name N...AA322 - 346329 - 353
17LYSLYSGLNGLN(chain 'A' and ((resid 6 through 11 and (name N...AA352 - 483359 - 490
18TRPTRPILEILE(chain 'A' and ((resid 6 through 11 and (name N...AA485 - 595492 - 602
19SERSERHISHIS(chain 'A' and ((resid 6 through 11 and (name N...AA598 - 635605 - 642
110GLYGLYPROPRO(chain 'A' and ((resid 6 through 11 and (name N...AA638 - 732645 - 739
111PHEPHEMETMET(chain 'A' and ((resid 6 through 11 and (name N...AA734 - 750741 - 757
112ARGARGLEULEU(chain 'A' and ((resid 6 through 11 and (name N...AA755 - 887762 - 894
113LEULEUSERSER(chain 'A' and ((resid 6 through 11 and (name N...AA889 - 922896 - 929
114GLYGLYGLYGLY(chain 'A' and ((resid 6 through 11 and (name N...AA947 - 967954 - 974
215LEULEULEULEU(chain 'B' and ((resid 6 through 11 and (name N...BB6 - 13913 - 146
216GLUGLUPROPRO(chain 'B' and ((resid 6 through 11 and (name N...BB141 - 154148 - 161
217GLUGLUVALVAL(chain 'B' and ((resid 6 through 11 and (name N...BB156 - 178163 - 185
218ARGARGTHRTHR(chain 'B' and ((resid 6 through 11 and (name N...BB180 - 300187 - 307
219ASPASPGLUGLU(chain 'B' and ((resid 6 through 11 and (name N...BB302 - 320309 - 327
220LEULEUSERSER(chain 'B' and ((resid 6 through 11 and (name N...BB322 - 346329 - 353
221LYSLYSGLNGLN(chain 'B' and ((resid 6 through 11 and (name N...BB352 - 483359 - 490
222TRPTRPILEILE(chain 'B' and ((resid 6 through 11 and (name N...BB485 - 595492 - 602
223SERSERHISHIS(chain 'B' and ((resid 6 through 11 and (name N...BB598 - 635605 - 642
224GLYGLYPROPRO(chain 'B' and ((resid 6 through 11 and (name N...BB638 - 732645 - 739
225PHEPHEMETMET(chain 'B' and ((resid 6 through 11 and (name N...BB734 - 750741 - 757
226ARGARGLEULEU(chain 'B' and ((resid 6 through 11 and (name N...BB755 - 887762 - 894
227LEULEUSERSER(chain 'B' and ((resid 6 through 11 and (name N...BB889 - 922896 - 929
228GLYGLYGLYGLY(chain 'B' and ((resid 6 through 11 and (name N...BB947 - 967954 - 974
329LEULEULEULEU(chain 'C' and ((resid 6 through 11 and (name N...CC6 - 13913 - 146
330GLUGLUPROPRO(chain 'C' and ((resid 6 through 11 and (name N...CC141 - 154148 - 161
331GLUGLUVALVAL(chain 'C' and ((resid 6 through 11 and (name N...CC156 - 178163 - 185
332ARGARGTHRTHR(chain 'C' and ((resid 6 through 11 and (name N...CC180 - 300187 - 307
333ASPASPGLUGLU(chain 'C' and ((resid 6 through 11 and (name N...CC302 - 320309 - 327
334LEULEUSERSER(chain 'C' and ((resid 6 through 11 and (name N...CC322 - 346329 - 353
335LYSLYSGLNGLN(chain 'C' and ((resid 6 through 11 and (name N...CC352 - 483359 - 490
336TRPTRPILEILE(chain 'C' and ((resid 6 through 11 and (name N...CC485 - 595492 - 602
337SERSERHISHIS(chain 'C' and ((resid 6 through 11 and (name N...CC598 - 635605 - 642
338GLYGLYPROPRO(chain 'C' and ((resid 6 through 11 and (name N...CC638 - 732645 - 739
339PHEPHEMETMET(chain 'C' and ((resid 6 through 11 and (name N...CC734 - 750741 - 757
340ARGARGLEULEU(chain 'C' and ((resid 6 through 11 and (name N...CC755 - 887762 - 894
341LEULEUSERSER(chain 'C' and ((resid 6 through 11 and (name N...CC889 - 922896 - 929
342GLYGLYGLYGLY(chain 'C' and ((resid 6 through 11 and (name N...CC947 - 967954 - 974
443LEULEULEULEU(chain 'D' and ((resid 6 through 11 and (name N...DD6 - 13913 - 146
444GLUGLUPROPRO(chain 'D' and ((resid 6 through 11 and (name N...DD141 - 154148 - 161
445GLUGLUVALVAL(chain 'D' and ((resid 6 through 11 and (name N...DD156 - 178163 - 185
446ARGARGTHRTHR(chain 'D' and ((resid 6 through 11 and (name N...DD180 - 300187 - 307
447ASPASPGLUGLU(chain 'D' and ((resid 6 through 11 and (name N...DD302 - 320309 - 327
448LEULEUSERSER(chain 'D' and ((resid 6 through 11 and (name N...DD322 - 346329 - 353
449LYSLYSGLNGLN(chain 'D' and ((resid 6 through 11 and (name N...DD352 - 483359 - 490
450TRPTRPILEILE(chain 'D' and ((resid 6 through 11 and (name N...DD485 - 595492 - 602
451SERSERHISHIS(chain 'D' and ((resid 6 through 11 and (name N...DD598 - 635605 - 642
452GLYGLYPROPRO(chain 'D' and ((resid 6 through 11 and (name N...DD638 - 732645 - 739
453PHEPHEMETMET(chain 'D' and ((resid 6 through 11 and (name N...DD734 - 750741 - 757
454ARGARGLEULEU(chain 'D' and ((resid 6 through 11 and (name N...DD755 - 887762 - 894
455LEULEUSERSER(chain 'D' and ((resid 6 through 11 and (name N...DD889 - 922896 - 929
456GLYGLYGLYGLY(chain 'D' and ((resid 6 through 11 and (name N...DD947 - 967954 - 974
557LEULEULEULEU(chain 'E' and ((resid 6 through 11 and (name N...EE6 - 13913 - 146
558GLUGLUPROPRO(chain 'E' and ((resid 6 through 11 and (name N...EE141 - 154148 - 161
559GLUGLUVALVAL(chain 'E' and ((resid 6 through 11 and (name N...EE156 - 178163 - 185
560ARGARGTHRTHR(chain 'E' and ((resid 6 through 11 and (name N...EE180 - 300187 - 307
561ASPASPGLUGLU(chain 'E' and ((resid 6 through 11 and (name N...EE302 - 320309 - 327
562LEULEUSERSER(chain 'E' and ((resid 6 through 11 and (name N...EE322 - 346329 - 353
563LYSLYSGLNGLN(chain 'E' and ((resid 6 through 11 and (name N...EE352 - 483359 - 490
564TRPTRPILEILE(chain 'E' and ((resid 6 through 11 and (name N...EE485 - 595492 - 602
565SERSERHISHIS(chain 'E' and ((resid 6 through 11 and (name N...EE598 - 635605 - 642
566GLYGLYPROPRO(chain 'E' and ((resid 6 through 11 and (name N...EE638 - 732645 - 739
567PHEPHEMETMET(chain 'E' and ((resid 6 through 11 and (name N...EE734 - 750741 - 757
568ARGARGLEULEU(chain 'E' and ((resid 6 through 11 and (name N...EE755 - 887762 - 894
569LEULEUSERSER(chain 'E' and ((resid 6 through 11 and (name N...EE889 - 922896 - 929
570GLYGLYGLYGLY(chain 'E' and ((resid 6 through 11 and (name N...EE947 - 967954 - 974
671LEULEULEULEU(chain 'F' and ((resid 6 through 11 and (name N...FF6 - 13913 - 146
672GLUGLUPROPRO(chain 'F' and ((resid 6 through 11 and (name N...FF141 - 154148 - 161
673GLUGLUVALVAL(chain 'F' and ((resid 6 through 11 and (name N...FF156 - 178163 - 185
674ARGARGTHRTHR(chain 'F' and ((resid 6 through 11 and (name N...FF180 - 300187 - 307
675ASPASPGLUGLU(chain 'F' and ((resid 6 through 11 and (name N...FF302 - 320309 - 327
676LEULEUSERSER(chain 'F' and ((resid 6 through 11 and (name N...FF322 - 346329 - 353
677LYSLYSGLNGLN(chain 'F' and ((resid 6 through 11 and (name N...FF352 - 483359 - 490
678TRPTRPILEILE(chain 'F' and ((resid 6 through 11 and (name N...FF485 - 595492 - 602
679SERSERHISHIS(chain 'F' and ((resid 6 through 11 and (name N...FF598 - 635605 - 642
680GLYGLYPROPRO(chain 'F' and ((resid 6 through 11 and (name N...FF638 - 732645 - 739
681PHEPHEMETMET(chain 'F' and ((resid 6 through 11 and (name N...FF734 - 750741 - 757
682ARGARGLEULEU(chain 'F' and ((resid 6 through 11 and (name N...FF755 - 887762 - 894
683LEULEUSERSER(chain 'F' and ((resid 6 through 11 and (name N...FF889 - 922896 - 929
684GLYGLYGLYGLY(chain 'F' and ((resid 6 through 11 and (name N...FF947 - 967954 - 974
785LEULEULEULEU(chain 'G' and ((resid 6 through 11 and (name N...GG6 - 13913 - 146
786GLUGLUPROPRO(chain 'G' and ((resid 6 through 11 and (name N...GG141 - 154148 - 161
787GLUGLUVALVAL(chain 'G' and ((resid 6 through 11 and (name N...GG156 - 178163 - 185
788ARGARGTHRTHR(chain 'G' and ((resid 6 through 11 and (name N...GG180 - 300187 - 307
789ASPASPGLUGLU(chain 'G' and ((resid 6 through 11 and (name N...GG302 - 320309 - 327
790LEULEUSERSER(chain 'G' and ((resid 6 through 11 and (name N...GG322 - 346329 - 353
791LYSLYSGLNGLN(chain 'G' and ((resid 6 through 11 and (name N...GG352 - 483359 - 490
792TRPTRPILEILE(chain 'G' and ((resid 6 through 11 and (name N...GG485 - 595492 - 602
793SERSERHISHIS(chain 'G' and ((resid 6 through 11 and (name N...GG598 - 635605 - 642
794GLYGLYPROPRO(chain 'G' and ((resid 6 through 11 and (name N...GG638 - 732645 - 739
795PHEPHEMETMET(chain 'G' and ((resid 6 through 11 and (name N...GG734 - 750741 - 757
796ARGARGLEULEU(chain 'G' and ((resid 6 through 11 and (name N...GG755 - 887762 - 894
797LEULEUSERSER(chain 'G' and ((resid 6 through 11 and (name N...GG889 - 922896 - 929
798GLYGLYGLYGLY(chain 'G' and ((resid 6 through 11 and (name N...GG947 - 967954 - 974
899LEULEULEULEU(chain 'H' and ((resid 6 through 11 and (name N...HH6 - 13913 - 146
8100GLUGLUPROPRO(chain 'H' and ((resid 6 through 11 and (name N...HH141 - 154148 - 161
8101GLUGLUVALVAL(chain 'H' and ((resid 6 through 11 and (name N...HH156 - 178163 - 185
8102ARGARGTHRTHR(chain 'H' and ((resid 6 through 11 and (name N...HH180 - 300187 - 307
8103ASPASPGLUGLU(chain 'H' and ((resid 6 through 11 and (name N...HH302 - 320309 - 327
8104LEULEUSERSER(chain 'H' and ((resid 6 through 11 and (name N...HH322 - 346329 - 353
8105LYSLYSGLNGLN(chain 'H' and ((resid 6 through 11 and (name N...HH352 - 483359 - 490
8106TRPTRPILEILE(chain 'H' and ((resid 6 through 11 and (name N...HH485 - 595492 - 602
8107SERSERHISHIS(chain 'H' and ((resid 6 through 11 and (name N...HH598 - 635605 - 642
8108GLYGLYPROPRO(chain 'H' and ((resid 6 through 11 and (name N...HH638 - 732645 - 739
8109PHEPHEMETMET(chain 'H' and ((resid 6 through 11 and (name N...HH734 - 750741 - 757
8110ARGARGLEULEU(chain 'H' and ((resid 6 through 11 and (name N...HH755 - 887762 - 894
8111LEULEUSERSER(chain 'H' and ((resid 6 through 11 and (name N...HH889 - 922896 - 929
8112GLYGLYGLYGLY(chain 'H' and ((resid 6 through 11 and (name N...HH947 - 967954 - 974

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要素

#1: タンパク質
Phosphoenolpyruvate carboxylase 1 / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide


分子量: 111398.164 Da / 分子数: 8 / 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: PPC1, p107, At1g53310, F12M16.21 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q9MAH0, phosphoenolpyruvate carboxylase
#2: 化合物
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / L-りんご酸


分子量: 134.087 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C4H6O5 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 40 / 由来タイプ: 合成 / 式: C4H10O3
#4: 化合物...
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 23 / 由来タイプ: 合成 / 式: Cl
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 133 / 由来タイプ: 天然 / 式: H2O
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: 4.1 Å3/Da / 溶媒含有率: 70.03 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 7.5
詳細: 30%PEG400, 0.1 M Hepes Sodium Salt pH 7.5, 200mM Magnesium Chloride

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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: SOLEIL / ビームライン: PROXIMA 2 / 波長: 0.981 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年12月16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: 0.981 Å / 相対比: 1
反射解像度: 3.142→50 Å / Num. obs: 237667 / % possible obs: 99.3 % / 冗長度: 7.11 % / Biso Wilson estimate: 82.2502477245 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.292 / Net I/σ(I): 6.94
反射 シェル解像度: 3.143→3.33 Å / 冗長度: 6.42 % / Rmerge(I) obs: 2.102 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 36978 / CC1/2: 0.352 / % possible all: 96.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1_2575精密化
XDSデータ削減
XDS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: 3.14239899937→48.9254741206 Å / SU ML: 0.527092632809 / 交差検証法: FREE R-VALUE / σ(F): 1.3280661634 / 位相誤差: 25.6059321202
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.239756715239 11875 4.99962108135 %
Rwork0.202062209888 225643 -
obs0.20393187438 237518 99.3022196022 %
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: 75.9200195511 Å2
精密化ステップサイクル: LAST / 解像度: 3.14239899937→48.9254741206 Å
タンパク質核酸リガンド溶媒全体
原子数58490 0 295 133 58918
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0057783318625660198
X-RAY DIFFRACTIONf_angle_d0.83680890531681660
X-RAY DIFFRACTIONf_chiral_restr0.04700905103519163
X-RAY DIFFRACTIONf_plane_restr0.0059871953906210633
X-RAY DIFFRACTIONf_dihedral_angle_d12.676923545936274
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1424-3.17810.4681740872363190.4442247365366051X-RAY DIFFRACTION81.0123362584
3.1781-3.21550.4181353951614010.3805801142097616X-RAY DIFFRACTION99.9875280619
3.2155-3.25470.3587862868093980.3453764594717560X-RAY DIFFRACTION99.9623162919
3.2547-3.29590.3616542176453960.3330038650787530X-RAY DIFFRACTION99.9621642073
3.2959-3.33920.3580534025264000.323667113177587X-RAY DIFFRACTION99.9249343175
3.3392-3.3850.348330149693960.3083832208487524X-RAY DIFFRACTION99.9495204442
3.385-3.43330.3403685143254000.3052509178197591X-RAY DIFFRACTION99.9499687305
3.4333-3.48450.324044903673950.2887578364227505X-RAY DIFFRACTION99.9493927126
3.4845-3.5390.300734746194010.2757956541457631X-RAY DIFFRACTION99.9626633479
3.539-3.5970.2827913874173960.2599474287017539X-RAY DIFFRACTION99.9496158206
3.597-3.6590.3190377854153960.2557814460637530X-RAY DIFFRACTION99.9621642073
3.659-3.72550.2825013007743990.2550385354417570X-RAY DIFFRACTION99.9372962127
3.7255-3.79710.2690590824143960.2325686196277539X-RAY DIFFRACTION99.9622071051
3.7971-3.87460.265948435654000.2174309154347595X-RAY DIFFRACTION99.9499937492
3.8746-3.95880.2360985676823980.198817481367555X-RAY DIFFRACTION99.9497297977
3.9588-4.05090.2197658402453980.1863535241827566X-RAY DIFFRACTION100
4.0509-4.15210.2426772434333980.1943894089157577X-RAY DIFFRACTION99.9749279178
4.1521-4.26430.2244148511483980.1791849688647563X-RAY DIFFRACTION99.9497802888
4.2643-4.38970.2096608009893980.1733819410067556X-RAY DIFFRACTION99.9748617396
4.3897-4.53130.1968243116223990.1566667621787576X-RAY DIFFRACTION99.912302681
4.5313-4.69320.1935033001693990.1461552271747574X-RAY DIFFRACTION99.9122807018
4.6932-4.88090.1821380417483990.1497969738697578X-RAY DIFFRACTION99.8998121478
4.8809-5.10280.2060481092463990.159688004087559X-RAY DIFFRACTION99.9372095944
5.1028-5.37150.206527724253980.1583991714527563X-RAY DIFFRACTION99.9497802888
5.3715-5.70760.2127468673593990.1664190492247591X-RAY DIFFRACTION99.974974975
5.7076-6.14750.2451579620754010.1893033639167612X-RAY DIFFRACTION99.9875218368
6.1475-6.76470.2253966433913990.1797913869957595X-RAY DIFFRACTION99.9499874969
6.7647-7.74030.2047479018733990.1604988619447597X-RAY DIFFRACTION99.9375078115
7.7403-9.73930.1537023571624000.1313437755767602X-RAY DIFFRACTION99.9001248439
9.7393-48.92547412060.215114366934000.1896789164127611X-RAY DIFFRACTION99.2197176121

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る