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- PDB-7kr7: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant w... -

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基本情報

登録情報
データベース: PDB / ID: 7kr7
タイトルDihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant with pyruvate bound in the active site and L-lysine at the allosteric site
要素4-hydroxy-tetrahydrodipicolinate synthase
キーワードLYASE / Dihydrodipicolinate synthase
機能・相同性
機能・相同性情報


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
類似検索 - 分子機能
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
類似検索 - ドメイン・相同性
ACETATE ION / LYSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
類似検索 - 構成要素
生物種Campylobacter jejuni subsp. jejuni serotype O:2 (カンピロバクター)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.22 Å
データ登録者Saran, S. / Sanders, D.A.R.
資金援助 カナダ, 1件
組織認可番号国
Natural Sciences and Engineering Research Council (NSERC, Canada) カナダ
引用ジャーナル: To Be Published
タイトル: ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS
著者: Saran, S. / Skovpen, Y. / Yazdi, M.M. / Palmer, D.R.J. / Sanders, D.A.R.
履歴
登録2020年11月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年11月24日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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
改定 1.22023年11月29日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)208,34146
ポリマ－204,7096
非ポリマー3,63240
水20,5911143
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,32514
ポリマ－68,2362
非ポリマー1,08812
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-13 kcal/mol
Surface area21080 Å2
手法PISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,60318
ポリマ－68,2362
非ポリマー1,36716
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-12 kcal/mol
Surface area21180 Å2
手法PISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,41314
ポリマ－68,2362
非ポリマー1,17712
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-22 kcal/mol
Surface area21690 Å2
手法PISA
単位格子
Length a, b, c (Å)85.800, 231.240, 199.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 3 through 204 or (resid 205...
21(chain B and (resid 3 through 204 or (resid 205...
31(chain C and (resid 3 through 165 or (resid 166...
41(chain D and (resid 3 through 165 or (resid 166...
51(chain E and (resid 3 through 165 or (resid 166...
61(chain F and (resid 3 through 204 or (resid 205...

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
11LYSLYSLYSLYS(chain A and (resid 3 through 204 or (resid 205...AA3 - 20415 - 216
12GLYGLYGLYGLY(chain A and (resid 3 through 204 or (resid 205...AA205217
13LYSLYSPHEPHE(chain A and (resid 3 through 204 or (resid 205...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 204 or (resid 205...AA3 - 29815 - 310
21LYSLYSLYSLYS(chain B and (resid 3 through 204 or (resid 205...BB3 - 20415 - 216
22GLYGLYGLYGLY(chain B and (resid 3 through 204 or (resid 205...BB205217
23LYSLYSPHEPHE(chain B and (resid 3 through 204 or (resid 205...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 204 or (resid 205...BB3 - 29815 - 310
31LYSLYSVALVAL(chain C and (resid 3 through 165 or (resid 166...CC3 - 16515 - 177
32KPIKPIKPIKPI(chain C and (resid 3 through 165 or (resid 166...CC166178
33LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
36LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
37LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
38LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
39LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
310LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
311LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
312LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
313LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
314LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
315LYSLYSPHEPHE(chain C and (resid 3 through 165 or (resid 166...CC3 - 29815 - 310
41LYSLYSVALVAL(chain D and (resid 3 through 165 or (resid 166...DD3 - 16515 - 177
42KPIKPIKPIKPI(chain D and (resid 3 through 165 or (resid 166...DD166178
43LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
46LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
47LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
48LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
49LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
410LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
411LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
412LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
413LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
414LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
415LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
51LYSLYSVALVAL(chain E and (resid 3 through 165 or (resid 166...EE3 - 16515 - 177
52KPIKPIKPIKPI(chain E and (resid 3 through 165 or (resid 166...EE166178
53LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
57LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
58LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
59LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
510LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
511LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
512LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
513LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
514LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
515LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
61LYSLYSLYSLYS(chain F and (resid 3 through 204 or (resid 205...FF3 - 20415 - 216
62GLYGLYGLYGLY(chain F and (resid 3 through 204 or (resid 205...FF205217
63ASPASPPHEPHE(chain F and (resid 3 through 204 or (resid 205...FF2 - 29814 - 310
64ASPASPPHEPHE(chain F and (resid 3 through 204 or (resid 205...FF2 - 29814 - 310

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要素

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タンパク質 , 1種, 6分子 ABCDEF

#1: タンパク質
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


分子量: 34118.191 Da / 分子数: 6 / 変異: H56A / 由来タイプ: 組換発現
由来: (組換発現) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (カンピロバクター)
株: ATCC 700819 / NCTC 11168 / 遺伝子: dapA, Cj0806 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

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非ポリマー , 8種, 1183分子

#2: 化合物
ChemComp-LYS / LYSINE / 2-アンモニオ-2-デアミノ-L-リシン


タイプ: L-peptide linking / 分子量: 147.195 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C6H15N2O2 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C6H14O4 / タイプ: SUBJECT OF INVESTIGATION
#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: 10 / 由来タイプ: 合成 / 式: C2H6O2 / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C2H3O2 / タイプ: SUBJECT OF INVESTIGATION
#7: 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: 5 / 由来タイプ: 合成 / 式: C4H10O3 / タイプ: SUBJECT OF INVESTIGATION
#8: 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: 1 / 由来タイプ: 合成 / 式: C3H8O3 / タイプ: SUBJECT OF INVESTIGATION
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1143 / 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: 2.42 Å3/Da / 溶媒含有率: 49.12 %
結晶化温度: 288.15 K / 手法: マイクロバッチ法
詳細: 0.3 M Magnesium acetate, 12 % PEG 8000, 0.1 M Sodium acetate (pH 7.4)

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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: CLSI / ビームライン: 08ID-1 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2019年8月1日
放射モノクロメーター: Double beam / 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: 0.9795 Å / 相対比: 1
反射解像度: 2.22→45.8 Å / Num. obs: 97699 / % possible obs: 99.7 % / 冗長度: 15 % / CC1/2: 0.995 / Net I/σ(I): 14.46
反射 シェル解像度: 2.22→2.29 Å / Rmerge(I) obs: 0.228 / Num. unique obs: 9423 / % possible all: 97.16

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHENIX1.17.1_3660精密化
PDB_EXTRACT3.27データ抽出
HKL-3000データ削減
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4LY8

4ly8


解像度: 2.22→45.8 Å / SU ML: 0.18 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 17.63 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1893 4884 5 %
Rwork0.1489 92801 -
obs0.1509 97685 99.66 %
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: 110.23 Å2 / Biso mean: 25.9063 Å2 / Biso min: 0.7 Å2
精密化ステップサイクル: final / 解像度: 2.22→45.8 Å
タンパク質核酸リガンド溶媒全体
原子数13577 0 180 1143 14900
Biso mean--38.07 33.16 -
残基数----1783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5358X-RAY DIFFRACTION1.82TORSIONAL
12B5358X-RAY DIFFRACTION1.82TORSIONAL
13C5358X-RAY DIFFRACTION1.82TORSIONAL
14D5358X-RAY DIFFRACTION1.82TORSIONAL
15E5358X-RAY DIFFRACTION1.82TORSIONAL
16F5358X-RAY DIFFRACTION1.82TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.22-2.250.21971540.1588293495
2.25-2.270.2081560.1543296997
2.27-2.30.23391610.1572304999
2.3-2.330.22691610.15643070100
2.33-2.360.21021610.15123046100
2.36-2.390.21721620.1523085100
2.39-2.430.20461620.14833074100
2.43-2.460.19471640.14423117100
2.46-2.50.18421600.143039100
2.5-2.540.20631630.14253090100
2.54-2.590.18581610.13723070100
2.59-2.630.18451630.14063088100
2.63-2.680.20791630.1423095100
2.68-2.740.18881620.14523083100
2.74-2.80.19061620.1453077100
2.8-2.860.19671630.15413104100
2.86-2.930.20981630.15733090100
2.93-3.010.19541600.16543051100
3.01-3.10.19711640.15983114100
3.1-3.20.21961630.16033085100
3.2-3.320.22871630.16953112100
3.32-3.450.18821640.1693107100
3.45-3.610.20831640.16333112100
3.61-3.80.17171620.14423087100
3.8-4.030.18121650.13713135100
4.03-4.340.1741660.13293143100
4.34-4.780.16781650.12733139100
4.78-5.470.16081650.14423140100
5.47-6.890.17041680.16193200100
6.89-100.14171740.13923296100
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)
11.2310.15770.33452.1586-0.22361.62780.01-0.11060.11360.22690.0130.1404-0.0912-0.1057-0.02180.1910.0520.01080.21780.04940.2495-76.302-65.49619.504
20.6832-0.30851.05236.2707-1.20882.24060.0544-0.26770.02860.12850.03480.5846-0.0681-0.3199-0.17330.13910.05580.03220.27130.07960.3246-84.854-68.98618.126
30.2323-0.61850.09794.82670.52911.0644-0.05640.14240.0495-0.0009-0.1060.2824-0.0535-0.28220.05050.12580.0253-0.01720.24110.07290.2639-81.817-73.74410.487
40.8712-0.1925-0.43021.9193-0.04341.1231-0.01550.0937-0.0076-0.19720.090.1730.0599-0.1237-0.04530.1723-0.0265-0.02540.16160.0440.1604-73.034-81.6627.828
50.2948-0.0241-0.22161.37540.53160.7822-0.0313-0.00760.0531-0.03490.03030.01330.0354-0.05-0.01220.1748-0.0068-0.01880.21480.05150.198-63.401-72.4314.413
62.57950.1361-0.18341.7169-0.22323.4936-0.00810.0240.39-0.04960.0705-0.1075-0.1960.1103-0.05960.15960.0074-0.01890.12110.00610.2364-57.768-59.2813.319
71.18420.19980.14214.0023-1.18962.057-0.0469-0.10750.04190.51410.10220.0258-0.1575-0.0804-0.04320.23780.02060.00230.19230.00740.1412-65.416-65.87331.115
81.4215-0.34360.05671.36490.17641.2851-0.00960.1385-0.0105-0.1931-0.0423-0.15610.120.16790.03340.1536-0.02740.02930.21720.08030.2381-25.788-78.301-2.478
91.1480.1996-0.37292.4789-2.51674.4937-0.0686-0.05080.18390.1433-0.0262-0.2303-0.29890.09420.13510.1481-0.0324-0.03870.19980.04090.3271-22.223-74.6058.302
100.7781-0.0483-0.47651.4234-0.28681.1095-0.1065-0.06590.18760.0689-0.0313-0.137-0.08930.0910.12730.1539-0.0038-0.04620.17790.03810.2195-30.913-76.3816.532
110.4304-0.25860.06350.97940.00431.9699-0.06460.00240.14240.10940.0169-0.1278-0.046-0.0550.05240.1676-0.0131-0.03590.19250.0390.2469-40.606-68.82810.385
121.6742-0.0206-0.28874.12580.26931.14020.00180.26820.2597-0.29530.07750.2039-0.077-0.0646-0.06760.1598-0.0161-0.01150.23070.07330.1824-46.346-69.83-5.498
131.9982-0.10320.2573.5034-1.05182.3909-0.04820.2269-0.0315-0.50510.0171-0.11420.297-0.12580.03060.21910.00510.01740.19220.02140.1445-38.63-88.299-8.899
142.11411.35991.04313.83771.12971.9806-0.02090.05020.06830.18270.0107-0.2166-0.10530.18280.02390.2110.0338-0.01130.24390.08870.1896-25.455-100.55728.112
150.91020.9308-0.90822.102-0.30111.2410.03930.0136-0.04470.2279-0.0394-0.0795-0.02720.2091-0.01880.19580.0156-0.03430.26280.08080.2516-24.291-100.43631.223
160.3035-0.8910.65254.3445-0.71632.2726-0.0459-0.283-0.1640.1650.0512-0.5388-0.03660.20930.05920.11120.0186-0.02840.24290.05770.2792-17.501-101.0824.254
170.6379-0.83861.10832.345-2.09254.1866-0.04160.0417-0.1318-0.08560.0316-0.07250.18340.11580.02120.15540.01940.04350.1720.03820.247-23.125-104.55617.468
181.2250.2101-0.09421.6734-0.350.9467-0.03720.0301-0.0123-0.19480.0352-0.14970.12690.08730.00320.18420.01070.02180.16410.03310.1538-33.388-101.37811.819
191.73040.7425-0.19562.16740.61932.8513-0.0671-0.0081-0.0471-0.08820.0122-0.12020.1320.05330.08620.20490.00070.00160.16680.03860.1955-39.655-108.15413.209
200.77270.19580.09690.4312-0.00210.9683-0.0382-0.073-0.058-0.01020.0250.00410.0402-0.0250.00560.20270.0190.00420.20930.05530.2143-42.332-107.8427.509
212.04980.4611-0.3015.7643-0.14461.4487-0.0726-0.3073-0.2010.23680.0770.0710.2907-0.0701-0.03110.19640.01660.00870.23630.0510.1324-45.212-104.13137.374
221.7720.5377-0.29362.1561-0.36242.3212-0.0141-0.22850.1380.282-0.0408-0.0782-0.2605-0.00920.02570.2219-0.0058-0.04730.23780.01750.1898-32.117-88.92238.085
231.3376-0.1583-0.08821.4602-0.11512.7909-0.06620.09670.0962-0.0417-0.01030.1996-0.1847-0.27380.04790.1697-0.0185-0.04520.28170.01620.2441-29.35-132.79438.735
240.6840.3054-0.38482.07560.24711.5272-0.0405-0.22270.11170.10660.0230.17660.0793-0.98-0.03840.1695-0.0302-0.020.45980.00760.2909-36.563-136.89942.853
251.2583-0.52040.371.4897-0.42791.5106-0.03180.1063-0.1425-0.16720.04360.10410.2869-0.2319-0.02230.1953-0.0719-0.0110.2044-0.02740.1611-25.225-148.70544.092
260.5581-0.4441-0.23121.021-0.10720.5891-0.06270.1184-0.003-0.00880.00530.04460.1754-0.0930.07420.2461-0.0408-0.03060.2393-0.01350.1845-15.038-147.17633.565
272.5670.44720.19811.87750.99852.5434-0.12680.47970.1388-0.31890.10940.1289-0.04980.0063-0.03830.2243-0.0076-0.03140.26470.04630.1915-13.349-132.18525.954
280.55680.1606-0.01641.2848-0.95053.76690.01590.10060.16570.0403-0.0405-0.042-0.2933-0.0750.06040.18010.0478-0.02070.18720.01840.224-18.693-121.38342.316
291.013-0.14480.16491.8160.04121.76250.0391-0.0169-0.0438-0.1610.06030.36110.1633-0.3418-0.09650.1632-0.04970.00130.23840.07240.2936-80.607-104.59522.513
300.71020.02380.13161.0764-0.18090.6632-0.0255-0.1106-0.08170.14540.07250.121-0.0311-0.1095-0.03390.16330.00140.02710.18690.06060.153-67.651-98.45131.685
312.8351-1.37181.48122.7608-3.10624.7212-0.1492-0.0788-0.2119-0.1240.0159-0.08330.1706-0.09760.1150.1969-0.01950.02050.1466-0.0080.2056-58.386-112.70618.733
321.0607-0.11960.29623.4009-0.93852.0105-0.04260.0919-0.1006-0.32110.19830.01240.17610.016-0.16910.2477-0.0439-0.04590.22530.00220.2232-71.526-106.6927.661
332.48061.4151.22623.40490.60711.95930.0841-0.1455-0.2146-0.0964-0.0588-0.11680.1898-0.19820.02440.2375-0.01140.04560.20190.01660.1444-20.639-149.43472.476
341.5986-0.74891.11740.80850.052.7375-0.0643-0.1296-0.19030.1210.04870.15560.2258-0.1809-0.00350.3037-0.04480.04580.21180.01920.2244-20.935-152.38874.069
352.1667-0.47712.40462.4472-1.2326.34590.0726-0.32190.04770.1856-0.04110.20330.4511-0.8013-0.14560.2799-0.0690.08370.2974-0.0020.2247-29.152-147.26473.07
361.4031-0.67320.741.9109-1.84574.1196-0.0734-0.21350.15440.2456-0.02350.103-0.1876-0.02850.05880.1981-0.01310.04320.1994-0.04140.1871-25.005-138.73271.805
371.19490.3177-0.1671.42070.30161.0728-0.0025-0.16460.130.04930.04830.06590.0374-0.0294-0.02510.17060.0108-0.00880.1708-0.00380.1622-16.963-133.83164.043
382.3667-0.6636-0.3032.69030.36881.9127-0.0212-0.12760.21780.0313-0.01430.0647-0.1357-0.01730.03290.1693-0.024-0.02930.1969-0.02120.1684-9.837-130.5769.164
390.98490.6253-0.21971.4355-0.90460.7552-0.0224-0.091-0.00310.0228-0.03220.02060.00190.04420.04230.20020.0219-0.00310.17870.00160.1204-3.374-140.43272.659
402.6022-0.01980.31882.43350.94533.0058-0.1395-0.3267-0.15190.26190.0642-0.09230.25170.22620.00530.29930.0498-0.00620.21880.04640.2075-0.804-151.78977.324
411.2589-0.96241.56721.5309-0.42492.695-0.0331-0.1683-0.12410.0775-0.05490.06810.4649-0.25710.0560.3303-0.05520.03010.18820.00460.2146-17.035-160.57763.099
423.56340.6099-0.23742.34740.34224.10250.0925-0.1014-0.6309-0.1328-0.0301-0.07570.9630.35750.00030.39320.0512-0.0190.15050.02310.3521-7.321-165.76568.584
430.0626-0.0660.09140.0762-0.1260.133-0.0064-0.05830.0511-0.0480.01890.0403-0.0098-0.0104-0.01850.1324-0.0212-0.00560.08310.03430.2459-43.281-105.6530.066
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:55 )A3 - 55
2X-RAY DIFFRACTION2( CHAIN A AND RESID 56:70 )A56 - 70
3X-RAY DIFFRACTION3( CHAIN A AND RESID 71:98 )A71 - 98
4X-RAY DIFFRACTION4( CHAIN A AND RESID 99:148 )A99 - 148
5X-RAY DIFFRACTION5( CHAIN A AND RESID 149:214 )A149 - 214
6X-RAY DIFFRACTION6( CHAIN A AND RESID 215:248 )A215 - 248
7X-RAY DIFFRACTION7( CHAIN A AND RESID 249:298 )A249 - 298
8X-RAY DIFFRACTION8( CHAIN B AND RESID 3:70 )B3 - 70
9X-RAY DIFFRACTION9( CHAIN B AND RESID 71:98 )B71 - 98
10X-RAY DIFFRACTION10( CHAIN B AND RESID 99:148 )B99 - 148
11X-RAY DIFFRACTION11( CHAIN B AND RESID 149:214 )B149 - 214
12X-RAY DIFFRACTION12( CHAIN B AND RESID 215:248 )B215 - 248
13X-RAY DIFFRACTION13( CHAIN B AND RESID 249:298 )B249 - 298
14X-RAY DIFFRACTION14( CHAIN C AND RESID 3:23 )C3 - 23
15X-RAY DIFFRACTION15( CHAIN C AND RESID 24:55 )C24 - 55
16X-RAY DIFFRACTION16( CHAIN C AND RESID 56:70 )C56 - 70
17X-RAY DIFFRACTION17( CHAIN C AND RESID 71:98 )C71 - 98
18X-RAY DIFFRACTION18( CHAIN C AND RESID 99:148 )C99 - 148
19X-RAY DIFFRACTION19( CHAIN C AND RESID 149:171 )C149 - 171
20X-RAY DIFFRACTION20( CHAIN C AND RESID 172:226 )C172 - 226
21X-RAY DIFFRACTION21( CHAIN C AND RESID 227:248 )C227 - 248
22X-RAY DIFFRACTION22( CHAIN C AND RESID 249:298 )C249 - 298
23X-RAY DIFFRACTION23( CHAIN D AND RESID 3:55 )D3 - 55
24X-RAY DIFFRACTION24( CHAIN D AND RESID 56:70 )D56 - 70
25X-RAY DIFFRACTION25( CHAIN D AND RESID 71:148 )D71 - 148
26X-RAY DIFFRACTION26( CHAIN D AND RESID 149:214 )D149 - 214
27X-RAY DIFFRACTION27( CHAIN D AND RESID 215:248 )D215 - 248
28X-RAY DIFFRACTION28( CHAIN D AND RESID 249:298 )D249 - 298
29X-RAY DIFFRACTION29( CHAIN E AND RESID 3:70 )E3 - 70
30X-RAY DIFFRACTION30( CHAIN E AND RESID 71:229 )E71 - 229
31X-RAY DIFFRACTION31( CHAIN E AND RESID 230:248 )E230 - 248
32X-RAY DIFFRACTION32( CHAIN E AND RESID 249:298 )E249 - 298
33X-RAY DIFFRACTION33( CHAIN F AND RESID 3:23 )F3 - 23
34X-RAY DIFFRACTION34( CHAIN F AND RESID 24:55 )F24 - 55
35X-RAY DIFFRACTION35( CHAIN F AND RESID 56:70 )F56 - 70
36X-RAY DIFFRACTION36( CHAIN F AND RESID 71:98 )F71 - 98
37X-RAY DIFFRACTION37( CHAIN F AND RESID 99:148 )F99 - 148
38X-RAY DIFFRACTION38( CHAIN F AND RESID 149:171 )F149 - 171
39X-RAY DIFFRACTION39( CHAIN F AND RESID 172:214 )F172 - 214
40X-RAY DIFFRACTION40( CHAIN F AND RESID 215:248 )F215 - 248
41X-RAY DIFFRACTION41( CHAIN F AND RESID 249:279 )F249 - 279
42X-RAY DIFFRACTION42( CHAIN F AND RESID 280:298 )F280 - 298
43X-RAY DIFFRACTION43( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )A301
44X-RAY DIFFRACTION43( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )C301
45X-RAY DIFFRACTION43( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )B301
46X-RAY DIFFRACTION43( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )E301
47X-RAY DIFFRACTION43( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )D301
48X-RAY DIFFRACTION43( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )F301

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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://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