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- PDB-6xgz: Crystal structure of E. coli MlaFB ABC transport subunits in the ... -

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IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 6xgz
タイトルCrystal structure of E. coli MlaFB ABC transport subunits in the monomeric state
要素
  • ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
  • Organic solvent ABC transporter ATP-binding protein
キーワードLIPID TRANSPORT / ABC transporters / MlaF / MlaB / bacterial outer membrane / ATPase / regulation / STAS domain
機能・相同性
機能・相同性情報


phospholipid transfer activity / intermembrane phospholipid transfer / phospholipid-translocating ATPase complex / phospholipid transport / トランスロカーゼ; 他の化合物の輸送を触媒; ヌクレオシド三リン酸の加水分解に伴う / ATPase-coupled transmembrane transporter activity / response to antibiotic / DNA damage response / ATP hydrolysis activity / ATP binding ...phospholipid transfer activity / intermembrane phospholipid transfer / phospholipid-translocating ATPase complex / phospholipid transport / トランスロカーゼ; 他の化合物の輸送を触媒; ヌクレオシド三リン酸の加水分解に伴う / ATPase-coupled transmembrane transporter activity / response to antibiotic / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
Probable ABC transporter ATP-binding protein MlaF/Mkl / : / : / STAS domain / STAS domain / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / ABC transporter-like, conserved site ...Probable ABC transporter ATP-binding protein MlaF/Mkl / : / : / STAS domain / STAS domain / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHATE ION / Intermembrane phospholipid transport system ATP-binding protein MlaF / Intermembrane phospholipid transport system binding protein MlaB / Organic solvent ABC transporter ATP-binding protein / Intermembrane phospholipid transport system binding protein MlaB
類似検索 - 構成要素
生物種Escherichia coli LAU-EC10 (大腸菌)
Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Chang, Y. / Bhabha, G. / Ekiert, D.C.
資金援助 米国, 5件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128777 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM112982 米国
Other privateDFS-20-16 米国
American Heart Association20POST35210202 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM088118 米国
引用ジャーナル: Elife / 年: 2020
タイトル: Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation.
著者: Kolich, L.R. / Chang, Y.T. / Coudray, N. / Giacometti, S.I. / MacRae, M.R. / Isom, G.L. / Teran, E.M. / Bhabha, G. / Ekiert, D.C.
履歴
登録2020年6月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月15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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Organic solvent ABC transporter ATP-binding protein
B: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
C: Organic solvent ABC transporter ATP-binding protein
D: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
E: Organic solvent ABC transporter ATP-binding protein
F: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
G: Organic solvent ABC transporter ATP-binding protein
H: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,86920
ポリマ－165,7718
非ポリマー1,09812
水18010
1
A: Organic solvent ABC transporter ATP-binding protein
B: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,7876
ポリマ－41,4432
非ポリマー3444
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-31 kcal/mol
Surface area17680 Å2
手法PISA
2
C: Organic solvent ABC transporter ATP-binding protein
D: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,7255
ポリマ－41,4432
非ポリマー2823
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-31 kcal/mol
Surface area17480 Å2
手法PISA
3
E: Organic solvent ABC transporter ATP-binding protein
F: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,7255
ポリマ－41,4432
非ポリマー2823
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-32 kcal/mol
Surface area18120 Å2
手法PISA
4
G: Organic solvent ABC transporter ATP-binding protein
H: ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,6334
ポリマ－41,4432
非ポリマー1902
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-32 kcal/mol
Surface area17870 Å2
手法PISA
単位格子
Length a, b, c (Å)78.270, 136.080, 261.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain B and ((resid -4 and (name N or name...
21(chain D and (resid -4 or resid -2 or resid...
31(chain F and (resid -4 or resid -2 or resid...
41(chain H and ((resid -4 and (name N or name...
12(chain C and (resid 4 through 17 or (resid 18...
22(chain E and (resid 4 through 17 or (resid 18...
32(chain G and (resid 4 through 83 or resid 85...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUGLUGLU(chain B and ((resid -4 and (name N or name...BB-48
121GLUGLUARGARG(chain B and ((resid -4 and (name N or name...BB-4 - 978 - 109
131GLUGLUARGARG(chain B and ((resid -4 and (name N or name...BB-4 - 978 - 109
141GLUGLUARGARG(chain B and ((resid -4 and (name N or name...BB-4 - 978 - 109
151GLUGLUARGARG(chain B and ((resid -4 and (name N or name...BB-4 - 978 - 109
211GLUGLUGLUGLU(chain D and (resid -4 or resid -2 or resid...DD-48
221LEULEULEULEU(chain D and (resid -4 or resid -2 or resid...DD-210
231PHEPHEPHEPHE(chain D and (resid -4 or resid -2 or resid...DD012
241SERSERSERSER(chain D and (resid -4 or resid -2 or resid...DD2 - 614 - 18
251METMETSERSER(chain D and (resid -4 or resid -2 or resid...DD8 - 4520 - 57
261VALVALARGARG(chain D and (resid -4 or resid -2 or resid...DD47 - 9759 - 109
311GLUGLUGLUGLU(chain F and (resid -4 or resid -2 or resid...FF-48
321LEULEULEULEU(chain F and (resid -4 or resid -2 or resid...FF-210
331PHEPHEPHEPHE(chain F and (resid -4 or resid -2 or resid...FF012
341SERSERSERSER(chain F and (resid -4 or resid -2 or resid...FF2 - 614 - 18
351METMETSERSER(chain F and (resid -4 or resid -2 or resid...FF8 - 4520 - 57
361VALVALARGARG(chain F and (resid -4 or resid -2 or resid...FF47 - 9759 - 109
411GLUGLUGLUGLU(chain H and ((resid -4 and (name N or name...HH-48
421GLUGLUARGARG(chain H and ((resid -4 and (name N or name...HH-4 - 978 - 109
431GLUGLUARGARG(chain H and ((resid -4 and (name N or name...HH-4 - 978 - 109
441GLUGLUARGARG(chain H and ((resid -4 and (name N or name...HH-4 - 978 - 109
451GLUGLUARGARG(chain H and ((resid -4 and (name N or name...HH-4 - 978 - 109
112SERSERTHRTHR(chain C and (resid 4 through 17 or (resid 18...CC4 - 174 - 17
122ARGARGARGARG(chain C and (resid 4 through 17 or (resid 18...CC1818
132SERSERPROPRO(chain C and (resid 4 through 17 or (resid 18...CC4 - 2674 - 267
212SERSERTHRTHR(chain E and (resid 4 through 17 or (resid 18...EE4 - 174 - 17
222ARGARGARGARG(chain E and (resid 4 through 17 or (resid 18...EE1818
232SERSERGLYGLY(chain E and (resid 4 through 17 or (resid 18...EE4 - 2684 - 268
312SERSERVALVAL(chain G and (resid 4 through 83 or resid 85...GG4 - 834 - 83
322LYSLYSALAALA(chain G and (resid 4 through 83 or resid 85...GG85 - 15085 - 150
332SERSERGLYGLY(chain G and (resid 4 through 83 or resid 85...GG4 - 2684 - 268
342SERSERGLYGLY(chain G and (resid 4 through 83 or resid 85...GG4 - 2684 - 268
352ALAALAPROPRO(chain G and (resid 4 through 83 or resid 85...GG215 - 238215 - 238
362PHEPHEPHEPHE(chain G and (resid 4 through 83 or resid 85...GG243243
372SERSERGLYGLY(chain G and (resid 4 through 83 or resid 85...GG4 - 2684 - 268
382SERSERGLYGLY(chain G and (resid 4 through 83 or resid 85...GG4 - 2684 - 268
392SERSERGLYGLY(chain G and (resid 4 through 83 or resid 85...GG4 - 2684 - 268

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 2種, 8分子 ACEGBDFH

#1: タンパク質
Organic solvent ABC transporter ATP-binding protein


分子量: 29128.801 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli LAU-EC10 (大腸菌)
遺伝子: V415_03760 / プラスミド: pBEL1307 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Rosetta2 / 参照: UniProt: V8KL36, UniProt: P63386*PLUS
#2: タンパク質
ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component / Lipid asymmetry maintenance protein MlaB / Phospholipid ABC transporter substrate-binding protein / ...Lipid asymmetry maintenance protein MlaB / Phospholipid ABC transporter substrate-binding protein / Phospholipid ABC transporter-binding protein / Putative anti-sigma factor antagonist / Putative phospholipid ABC transporter-binding protein MlaB


分子量: 12314.044 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: mlaB, yrbB, 55 / プラスミド: pBEL1307 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Rosetta2 / 参照: UniProt: W8T4U6, UniProt: P64602*PLUS

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非ポリマー , 4種, 22分子

#3: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 8 / 由来タイプ: 合成 / 式: PO4
#4: 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: 3 / 由来タイプ: 合成 / 式: C3H8O3
#5: 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: 1 / 由来タイプ: 合成 / 式: C2H6O2
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 10 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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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: 4.21 Å3/Da / 溶媒含有率: 70.75 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.6
詳細: 0.7 M NH4H2PO4, 0.07 M Na3 Cit pH5.6, 30 %v/v Glycerol

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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: 8.3.1 / 波長: 1.1158 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2016年8月12日
放射モノクロメーター: Water-cooled flat double Si(111) Khozu Monochromator
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: 1.1158 Å / 相対比: 1
反射解像度: 2.6→48.87 Å / Num. obs: 86874 / % possible obs: 92.07 % / 冗長度: 13.1 % / CC1/2: 1 / Net I/σ(I): 18.68
反射 シェル解像度: 2.6→2.693 Å / Num. unique obs: 8606 / CC1/2: 0.538

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
PDB_EXTRACT3.25データ抽出
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2OUK, 3F43

2ouk

3f43


解像度: 2.6→48.87 Å / SU ML: 0.38 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 29.03 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2374 1834 2.29 %Random
Rwork0.2025 78198 --
obs0.2033 80032 92.09 %-
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: 205.51 Å2 / Biso mean: 94.4207 Å2 / Biso min: 40.71 Å2
精密化ステップサイクル: final / 解像度: 2.6→48.87 Å
タンパク質核酸リガンド溶媒全体
原子数11090 0 62 10 11162
Biso mean--108.62 65.04 -
残基数----1456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11B1768X-RAY DIFFRACTION9.891TORSIONAL
12D1768X-RAY DIFFRACTION9.891TORSIONAL
13F1768X-RAY DIFFRACTION9.891TORSIONAL
14H1768X-RAY DIFFRACTION9.891TORSIONAL
21C3462X-RAY DIFFRACTION9.891TORSIONAL
22E3462X-RAY DIFFRACTION9.891TORSIONAL
23G3462X-RAY DIFFRACTION9.891TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.670.46391030.3984800490374
2.67-2.750.39411240.36395065518979
2.75-2.840.381210.32855263538481
2.84-2.940.30491340.29885643577788
2.94-3.060.30891400.28265774591490
3.06-3.20.32871420.27376053619594
3.2-3.360.24081450.2436224636996
3.36-3.570.26931510.22056381653298
3.57-3.850.25531530.20266416656999
3.85-4.240.20971480.17566530667899
4.24-4.850.18151550.150865496704100
4.85-6.110.20131560.193966256781100
6.11-48.870.22681620.17668757037100
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)
13.0639-1.9904-1.75633.0424-0.22224.5917-0.1216-0.73040.43010.2150.2784-0.54420.14641.1072-0.21030.4732-0.0689-0.07290.919-0.06940.718335.62449.448140.3235
22.572-2.37161.08852.8639-1.1722.75430.19920.071.1209-0.1854-0.2525-1.0276-0.77460.7751-0.00350.7068-0.24230.14060.74120.07470.990132.639619.125220.7488
30.6948-0.2242-0.58951.9725-0.44464.75220.0777-0.20280.30250.16150.0746-0.0879-0.42420.4676-0.14940.4134-0.1281-0.07890.5843-0.03450.62819.185216.222737.4127
41.03690.9417-0.71547.56612.56492.03640.0531-0.1323-0.15980.2135-0.4447-0.2990.6395-0.97070.63131.3207-0.30180.01641.2151-0.05330.785318.9006-4.54050.1801
52.0788-0.45151.53042.061-0.71011.8067-0.5441.2871-0.4113-0.5569-0.02650.62741.4323-2.10390.1480.9396-0.3349-0.04731.2956-0.02350.763714.155-1.5791.5526
66.21331.6724-3.25242.55750.18987.94780.71250.50910.1957-0.8212-0.5836-0.4824-0.2153-0.2786-0.17880.8372-0.0998-0.02020.76660.07390.690620.46634.47497.2639
75.95235.9874.37366.35974.59593.32790.3093-1.0659-0.7575-1.4553-0.8112-0.5511-1.3687-0.11310.51851.705-0.4360.02851.26260.10310.654416.84857.7102-2.9573
86.8211-1.09174.81512.49062.13357.62230.4836-1.2901-0.8903-1.2164-0.70160.7172-1.5632-1.46510.15091.2154-0.2334-0.42811.82420.10680.77117.37185.0672-2.2367
92.863-3.76921.61429.418-5.40753.38590.35940.1831-1.0886-0.7739-0.39450.82761.9196-2.33740.11230.8242-0.4019-0.18491.4042-0.23890.80098.64140.41178.8357
103.54640.5769-1.56475.26231.56597.01490.03080.2977-0.0521-0.5677-0.13940.1634-0.4108-0.92170.18630.6234-0.1021-0.0840.64830.11690.549313.78298.24969.0982
112.26440.1497-1.91983.5308-1.57032.33760.33770.3992-0.6215-0.2718-0.25190.82830.4645-2.17850.2410.7692-0.1206-0.16731.31350.0150.90334.80715.78086.7794
124.0038-1.0907-1.17052.84962.1198.82780.08280.4303-0.3553-0.0346-0.481.38180.7931-1.62590.24540.3302-0.146-0.0460.9689-0.03190.668510.31259.067621.3013
132.57394.0464.50788.83075.97418.3594-0.23252.14810.8686-0.0643-0.58831.302-0.0691-1.03270.90680.52660.0161-0.18321.12120.04761.01826.566215.189214.8373
145.6264-0.193-0.03324.555-0.8444.9546-0.10830.19740.4333-0.1693-0.04020.5218-0.4278-0.34230.17540.4914-0.0097-0.10470.48540.0610.6974-15.535517.32530.2793
152.2101-0.57833.66780.2198-1.14325.9329-0.2274-0.6721-0.17740.3678-0.00990.3135-0.1446-0.88090.48080.6719-0.0463-0.00640.7572-0.00650.7177-14.67414.533242.115
161.2968-0.71620.70150.7759-0.07913.3933-0.121-0.03180.16820.0778-0.02150.1753-0.084-0.2070.11650.4728-0.06270.00060.55250.03190.5794-0.92510.036941.4739
175.816-1.7939-2.61851.86560.53231.23040.3227-0.130.662-0.6087-0.13260.023-0.14810.3788-0.491.00040.0314-0.16190.6143-0.02021.06255.958130.84823.6886
184.98252.6005-2.43068.42622.76593.5265-0.50310.5016-0.5718-0.660.138-0.0090.7925-0.64170.22651.2634-0.10150.08110.898-0.01030.86113.0295-24.592926.4057
197.52234.3348-0.38538.92470.99962.08410.11320.3947-1.4737-1.13730.0916-1.0320.6916-0.4436-0.14530.93440.0501-0.02220.7336-0.0160.80447.3534-19.450528.6732
205.012.7946-3.66062.87080.92399.40280.06410.04460.22780.54610.4316-0.30540.2771-1.1212-0.53431.0244-0.1009-0.08580.9113-0.04410.9202-1.7726-15.662536.3233
214.00320.2902-4.10422.6502-0.35214.3079-0.2351-0.2555-1.06440.25910.216-0.28621.7366-0.31650.19031.51350.0575-0.01460.5056-0.02321.00719.8336-24.022137.6906
227.49843.6150.52362.01950.19368.62920.03670.57110.0099-0.71640.3114-0.19810.5852-0.0895-0.13650.71180.01810.10960.59330.0060.8117.8074-10.904728.3875
235.093-2.95192.42625.536-3.57966.6076-0.4744-0.6935-0.63171.23490.6922-0.89320.7003-0.0845-0.20731.04870.0231-0.1210.6101-0.01030.817412.0357-15.385340.8901
242.0202-2.4784-2.13698.70552.14984.33120.12010.19910.0411-0.30010.0283-0.41890.46870.4679-0.5180.5126-0.05630.11090.6678-0.00530.610112.2855-3.751932.2666
253.2768-3.8626-4.6864.61795.64016.8777-0.0101-0.9541-0.13580.10530.9133-1.7490.76621.6428-0.94540.56120.0843-0.07480.8044-0.13010.799614.8054-4.454241.2636
264.12750.56671.29482.86981.03733.44710.24930.0095-0.16610.14970.03060.63780.3315-2.1191-0.27590.75-0.06170.00591.82150.33791.0826-20.47671.906786.3131
270.76350.1564-0.23772.0127-0.78161.91140.1081-0.53310.59330.07910.42991.463-0.4572-1.4993-0.48220.93070.3840.0911.75340.20111.2658-18.709816.210183.7399
281.79270.71140.30383.7804-1.0794.4502-0.0074-0.131-0.03850.00940.26360.4648-0.0667-0.7677-0.28330.48550.1517-0.02940.68320.040.5584-3.656710.043481.3605
292.28121.68861.87931.6650.75383.8360.17640.63670.031-0.17290.3640.31220.301-0.3896-0.87951.4928-0.1836-0.09221.10490.04731.0677-3.7596-17.024896.6693
302.024-1.3916-0.10243.99873.36453.5209-0.2828-0.15640.90540.9698-0.01340.536-0.8478-0.44420.50511.48470.0988-0.04140.7912-0.05330.81020.258338.435104.3804
313.8343-1.10270.66618.86862.74677.59810.2391-0.84030.64790.8814-0.0577-0.6653-0.8842-0.64630.11271.20150.11980.00340.59710.03160.7235.259133.9906102.0431
323.89841.24211.58279.8823.94556.2482-0.8956-0.20740.8194-0.95750.36240.2097-1.4302-0.5310.40391.38210.2895-0.07610.5341-0.07510.66361.031236.238792.6374
339.793-6.78536.59384.7851-4.79855.0898-0.2920.6094-0.06260.8857-0.2971-1.06090.8844-0.19330.00151.39180.0749-0.25490.6845-0.30081.012115.223238.523597.6532
348.87132.1574-3.72297.9415-2.34134.62060.5657-0.9879-0.29821.51610.1398-0.1007-0.04320.777-0.32971.06870.252-0.11620.8992-0.08440.75855.013525.7586100.5049
355.3671.3994-0.61546.09270.86732.80410.41161.1032-0.05310.180.2017-0.86630.22920.3461-0.46130.99430.1548-0.05480.70470.0440.71329.832530.973289.3734
369.90836.1111-6.44394.1127-5.09127.7430.3671-0.8707-0.07680.70430.1291-0.632-0.0131.2849-0.3911.19560.1752-0.11390.9602-0.18430.832415.437628.983997.5411
378.8036-0.23162.03678.58582.62882.1174-0.3112-0.36180.43221.21070.65-0.54841.88510.7925-0.80991.17270.2181-0.15650.5729-0.00790.9327.426816.082192.9818
387.44071.35255.04247.28074.77039.92930.41020.52460.17480.15380.5014-1.39640.88051.7869-0.84840.81240.1771-0.10650.9271-0.13840.739213.598621.087587.8239
394.1851-0.598-3.0872.6088-0.31892.52850.10420.1113-0.47750.27790.3651-0.9881-0.07152.0734-0.47760.79840.4168-0.16661.7463-0.13851.157832.14191.640686.3019
404.08510.5794-0.50432.89210.57951.7061-0.10930.55330.1287-0.30920.2831-0.96960.44332.0858-0.22870.78230.4257-0.09711.5955-0.03710.89925.1281-0.581382.0182
410.4720.18890.13452.0541.99252.01770.56530.2189-0.53330.18080.2187-1.04991.32932.1093-0.34240.91920.6039-0.18012.1485-0.1531.159733.2695-3.276989.7829
420.325-0.3448-0.75892.8449-0.57272.86510.1047-0.3201-1.04770.3163-0.1698-1.54081.40461.1973-0.11291.35040.5398-0.24281.2561-0.01181.129425.4949-13.331397.9677
430.85160.2996-0.25452.5434-1.08342.58530.38420.1857-0.47590.0429-0.0622-0.12481.64710.4481-0.28251.32540.2394-0.25390.6094-0.05760.716511.0735-12.993698.8206
441.68491.13491.43062.6441-0.88656.7788-0.0350.48450.1878-0.39370.00040.08080.60471.5354-0.03880.61570.2433-0.06090.94820.01750.640316.64082.684578.183
451.9344-0.16710.67848.42174.7794.79680.4339-0.0816-0.0969-0.0009-0.034-1.0942-0.0490.2759-0.26670.68410.0491-0.02780.7872-0.05760.639410.776417.005171.8752
462.47521.34312.81224.07-2.10287.0530.1281-0.88040.19170.3393-0.06930.2786-1.10860.0445-0.25971.20540.01850.05231.0044-0.07390.744412.91325.5254127.0683
473.4891-0.31084.21612.04030.93696.1829-0.5343-0.79350.1096-0.02830.3069-0.6524-0.9270.2557-0.2470.9823-0.07940.080.8167-0.11550.655910.89995.1341118.9997
486.1692.01461.95312.4545-2.22055.50020.6302-0.3187-0.6643-0.2557-0.3252-1.22130.68550.9136-0.57721.20070.188-0.06840.7931-0.17970.863316.3061-4.6708118.5652
498.2038-5.6599-2.64456.02134.57974.44690.5395-0.88180.43941.38880.1768-0.07061.0807-0.6279-0.51221.50460.1168-0.08010.82990.00770.62238.9791-5.4098127.7812
509.3372-3.8725-0.96214.01181.79250.9105-0.008-0.8473-0.10280.24020.1320.2084-0.2835-1.5795-0.22651.18840.09620.20881.3279-0.18590.8580.96950.015127.8172
516.11422.2909-1.16542.942-3.84686.0373-0.1017-0.08870.52380.32310.15550.1195-1.1522-0.1361-0.23790.91810.198-0.04650.7724-0.08160.73269.08275.9547114.6874
525.0014-1.46240.82723.0265-0.36727.93920.2994-1.0765-0.9361-0.4425-0.04010.12791.0633-1.0103-0.1281.0649-0.1271-0.09380.56210.04320.74333.8744-5.8547117.563
533.60244.3238-5.4169.7728-6.19338.57170.2276-0.595-0.4085-0.02990.38511.24780.382-2.0124-0.56131.369-0.0201-0.0051.5974-0.00140.9783-4.288-2.4229124.5465
545.0691-0.4093-1.27753.8378-0.07732.090.05360.35850.6848-0.2962-0.08230.7029-0.1146-1.0539-0.3111.01870.1717-0.13550.609-0.0240.76963.44112.8855107.4509
557.4439-1.8951-0.55767.02092.94729.28990.28050.43-0.9961-0.6231-0.49530.91640.5475-1.9708-0.28870.8211-0.1318-0.08981.04090.12091.1202-2.9232-3.797109.4538
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 76 )A4 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 117 )A77 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 268 )A118 - 268
4X-RAY DIFFRACTION4chain 'B' and (resid -4 through 4 )B-4 - 4
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 12 )B5 - 12
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 30 )B13 - 30
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 35 )B31 - 35
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 40 )B36 - 40
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 45 )B41 - 45
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 67 )B46 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 78 )B68 - 78
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 87 )B79 - 87
13X-RAY DIFFRACTION13chain 'B' and (resid 88 through 97 )B88 - 97
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 76 )C4 - 76
15X-RAY DIFFRACTION15chain 'C' and (resid 77 through 101 )C77 - 101
16X-RAY DIFFRACTION16chain 'C' and (resid 102 through 237 )C102 - 237
17X-RAY DIFFRACTION17chain 'C' and (resid 238 through 267 )C238 - 267
18X-RAY DIFFRACTION18chain 'D' and (resid -4 through 4 )D-4 - 4
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 20 )D5 - 20
20X-RAY DIFFRACTION20chain 'D' and (resid 21 through 30 )D21 - 30
21X-RAY DIFFRACTION21chain 'D' and (resid 31 through 40 )D31 - 40
22X-RAY DIFFRACTION22chain 'D' and (resid 41 through 51 )D41 - 51
23X-RAY DIFFRACTION23chain 'D' and (resid 52 through 72 )D52 - 72
24X-RAY DIFFRACTION24chain 'D' and (resid 73 through 87 )D73 - 87
25X-RAY DIFFRACTION25chain 'D' and (resid 88 through 97 )D88 - 97
26X-RAY DIFFRACTION26chain 'E' and (resid 4 through 63 )E4 - 63
27X-RAY DIFFRACTION27chain 'E' and (resid 64 through 101 )E64 - 101
28X-RAY DIFFRACTION28chain 'E' and (resid 102 through 237 )E102 - 237
29X-RAY DIFFRACTION29chain 'E' and (resid 238 through 268 )E238 - 268
30X-RAY DIFFRACTION30chain 'F' and (resid -4 through 4 )F-4 - 4
31X-RAY DIFFRACTION31chain 'F' and (resid 5 through 20 )F5 - 20
32X-RAY DIFFRACTION32chain 'F' and (resid 21 through 35 )F21 - 35
33X-RAY DIFFRACTION33chain 'F' and (resid 36 through 40 )F36 - 40
34X-RAY DIFFRACTION34chain 'F' and (resid 41 through 51 )F41 - 51
35X-RAY DIFFRACTION35chain 'F' and (resid 52 through 67 )F52 - 67
36X-RAY DIFFRACTION36chain 'F' and (resid 68 through 78 )F68 - 78
37X-RAY DIFFRACTION37chain 'F' and (resid 79 through 87 )F79 - 87
38X-RAY DIFFRACTION38chain 'F' and (resid 88 through 97 )F88 - 97
39X-RAY DIFFRACTION39chain 'G' and (resid 4 through 20 )G4 - 20
40X-RAY DIFFRACTION40chain 'G' and (resid 21 through 46 )G21 - 46
41X-RAY DIFFRACTION41chain 'G' and (resid 47 through 76 )G47 - 76
42X-RAY DIFFRACTION42chain 'G' and (resid 77 through 101 )G77 - 101
43X-RAY DIFFRACTION43chain 'G' and (resid 102 through 194 )G102 - 194
44X-RAY DIFFRACTION44chain 'G' and (resid 195 through 247 )G195 - 247
45X-RAY DIFFRACTION45chain 'G' and (resid 248 through 268 )G248 - 268
46X-RAY DIFFRACTION46chain 'H' and (resid -4 through 12 )H-4 - 12
47X-RAY DIFFRACTION47chain 'H' and (resid 13 through 20 )H13 - 20
48X-RAY DIFFRACTION48chain 'H' and (resid 21 through 30 )H21 - 30
49X-RAY DIFFRACTION49chain 'H' and (resid 31 through 35 )H31 - 35
50X-RAY DIFFRACTION50chain 'H' and (resid 36 through 40 )H36 - 40
51X-RAY DIFFRACTION51chain 'H' and (resid 41 through 51 )H41 - 51
52X-RAY DIFFRACTION52chain 'H' and (resid 52 through 67 )H52 - 67
53X-RAY DIFFRACTION53chain 'H' and (resid 68 through 72 )H68 - 72
54X-RAY DIFFRACTION54chain 'H' and (resid 73 through 88 )H73 - 88
55X-RAY DIFFRACTION55chain 'H' and (resid 89 through 97 )H89 - 97

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万見について

-
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