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- PDB-7l4b: Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate ... -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 7l4b
タイトルDihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site in P1211 space group
要素4-hydroxy-tetrahydrodipicolinate synthase
キーワードLYASE
機能・相同性
機能・相同性情報


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / 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 / 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: 2.42 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: B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS.
著者: Saran, S. / Sanders, D.A.R.
履歴
登録2020年12月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年12月22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 / pdbx_initial_refinement_model
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
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
I: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)412,73537
ポリマ－410,22312
非ポリマー2,51225
水9,854547
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)137,44911
ポリマ－136,7414
非ポリマー7087
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-61 kcal/mol
Surface area39950 Å2
手法PISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
I: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)137,62413
ポリマ－136,7414
非ポリマー8839
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-63 kcal/mol
Surface area39350 Å2
手法PISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)137,66213
ポリマ－136,7414
非ポリマー9219
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-63 kcal/mol
Surface area39600 Å2
手法PISA
単位格子
Length a, b, c (Å)83.510, 200.360, 122.240
Angle α, β, γ (deg.)90.000, 109.830, 90.000
Int Tables number4
Space group name H-MP1211
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 75 or (resid 76...
21(chain B and (resid 3 through 75 or (resid 76...
31(chain C and (resid 3 through 75 or (resid 76...
41(chain D and (resid 3 through 165 or (resid 166...
51(chain E and (resid 3 through 75 or (resid 76...
61(chain F and (resid 3 through 75 or (resid 76...
71(chain G and (resid 3 through 75 or (resid 76...
81(chain H and (resid 3 through 75 or (resid 76...
91(chain I and (resid 3 through 75 or (resid 76...
101(chain J and (resid 3 through 75 or (resid 76...
111(chain K and (resid 3 through 75 or (resid 76...
121(chain L and (resid 3 through 75 or (resid 76...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 75 or (resid 76...A3 - 75
121(chain A and (resid 3 through 75 or (resid 76...A76
131(chain A and (resid 3 through 75 or (resid 76...A3 - 298
141(chain A and (resid 3 through 75 or (resid 76...A3 - 298
151(chain A and (resid 3 through 75 or (resid 76...A3 - 298
161(chain A and (resid 3 through 75 or (resid 76...A3 - 298
211(chain B and (resid 3 through 75 or (resid 76...B3 - 75
221(chain B and (resid 3 through 75 or (resid 76...B76
231(chain B and (resid 3 through 75 or (resid 76...B3 - 298
241(chain B and (resid 3 through 75 or (resid 76...B3 - 298
251(chain B and (resid 3 through 75 or (resid 76...B3 - 298
261(chain B and (resid 3 through 75 or (resid 76...B3 - 298
271(chain B and (resid 3 through 75 or (resid 76...B3 - 298
311(chain C and (resid 3 through 75 or (resid 76...C3 - 75
321(chain C and (resid 3 through 75 or (resid 76...C76
331(chain C and (resid 3 through 75 or (resid 76...C3 - 298
341(chain C and (resid 3 through 75 or (resid 76...C3 - 298
351(chain C and (resid 3 through 75 or (resid 76...C3 - 298
361(chain C and (resid 3 through 75 or (resid 76...C3 - 298
371(chain C and (resid 3 through 75 or (resid 76...C3 - 298
411(chain D and (resid 3 through 165 or (resid 166...D3 - 165
421(chain D and (resid 3 through 165 or (resid 166...D166
431(chain D and (resid 3 through 165 or (resid 166...D3 - 298
441(chain D and (resid 3 through 165 or (resid 166...D3 - 298
451(chain D and (resid 3 through 165 or (resid 166...D3 - 298
461(chain D and (resid 3 through 165 or (resid 166...D3 - 298
471(chain D and (resid 3 through 165 or (resid 166...D3 - 298
481(chain D and (resid 3 through 165 or (resid 166...D3 - 298
491(chain D and (resid 3 through 165 or (resid 166...D3 - 298
4101(chain D and (resid 3 through 165 or (resid 166...D3 - 298
4111(chain D and (resid 3 through 165 or (resid 166...D3 - 298
4121(chain D and (resid 3 through 165 or (resid 166...D3 - 298
511(chain E and (resid 3 through 75 or (resid 76...E3 - 75
521(chain E and (resid 3 through 75 or (resid 76...E76
531(chain E and (resid 3 through 75 or (resid 76...E5 - 298
541(chain E and (resid 3 through 75 or (resid 76...E5 - 298
551(chain E and (resid 3 through 75 or (resid 76...E5 - 298
561(chain E and (resid 3 through 75 or (resid 76...E5 - 298
571(chain E and (resid 3 through 75 or (resid 76...E5 - 298
611(chain F and (resid 3 through 75 or (resid 76...F3 - 75
621(chain F and (resid 3 through 75 or (resid 76...F76
631(chain F and (resid 3 through 75 or (resid 76...F3 - 298
641(chain F and (resid 3 through 75 or (resid 76...F3 - 298
651(chain F and (resid 3 through 75 or (resid 76...F3 - 298
661(chain F and (resid 3 through 75 or (resid 76...F3 - 298
711(chain G and (resid 3 through 75 or (resid 76...G3 - 75
721(chain G and (resid 3 through 75 or (resid 76...G76
731(chain G and (resid 3 through 75 or (resid 76...G3 - 298
741(chain G and (resid 3 through 75 or (resid 76...G3 - 298
751(chain G and (resid 3 through 75 or (resid 76...G3 - 298
761(chain G and (resid 3 through 75 or (resid 76...G3 - 298
771(chain G and (resid 3 through 75 or (resid 76...G3 - 298
781(chain G and (resid 3 through 75 or (resid 76...G3 - 298
811(chain H and (resid 3 through 75 or (resid 76...H3 - 75
821(chain H and (resid 3 through 75 or (resid 76...H76
831(chain H and (resid 3 through 75 or (resid 76...H3 - 298
841(chain H and (resid 3 through 75 or (resid 76...H3 - 298
851(chain H and (resid 3 through 75 or (resid 76...H3 - 298
861(chain H and (resid 3 through 75 or (resid 76...H3 - 298
871(chain H and (resid 3 through 75 or (resid 76...H3 - 298
911(chain I and (resid 3 through 75 or (resid 76...I3 - 75
921(chain I and (resid 3 through 75 or (resid 76...I76
931(chain I and (resid 3 through 75 or (resid 76...I3 - 298
941(chain I and (resid 3 through 75 or (resid 76...I3 - 298
951(chain I and (resid 3 through 75 or (resid 76...I3 - 298
961(chain I and (resid 3 through 75 or (resid 76...I3 - 298
971(chain I and (resid 3 through 75 or (resid 76...I3 - 298
1011(chain J and (resid 3 through 75 or (resid 76...J3 - 75
1021(chain J and (resid 3 through 75 or (resid 76...J76
1031(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1041(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1051(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1061(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1071(chain J and (resid 3 through 75 or (resid 76...J3 - 298
1111(chain K and (resid 3 through 75 or (resid 76...K3 - 75
1121(chain K and (resid 3 through 75 or (resid 76...K76
1131(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1141(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1151(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1161(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1171(chain K and (resid 3 through 75 or (resid 76...K3 - 298
1211(chain L and (resid 3 through 75 or (resid 76...L3 - 75
1221(chain L and (resid 3 through 75 or (resid 76...L76
1231(chain L and (resid 3 through 75 or (resid 76...L3 - 298
1241(chain L and (resid 3 through 75 or (resid 76...L3 - 298
1251(chain L and (resid 3 through 75 or (resid 76...L3 - 298
1261(chain L and (resid 3 through 75 or (resid 76...L3 - 298
1271(chain L and (resid 3 through 75 or (resid 76...L3 - 298

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要素

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タンパク質 , 1種, 12分子 ABCDEFGHIJKL

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


分子量: 34185.258 Da / 分子数: 12 / 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 , 5種, 572分子

#2: 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: 14 / 由来タイプ: 合成 / 式: C6H14O4 / 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: 7 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#4: 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 / 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: 1 / 由来タイプ: 合成 / 式: C2H6O2 / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 547 / 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: 2.35 Å3/Da / 溶媒含有率: 47.55 %
結晶化温度: 288.15 K / 手法: マイクロバッチ法 / pH: 7.4
詳細: 0.3 M Magnesium acetate, 10 % 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11月28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: 2.42→49.15 Å / Num. obs: 141419 / % possible obs: 98.47 % / 冗長度: 17 % / CC1/2: 0.994 / Rmerge(I) obs: 0.06747 / Net I/σ(I): 8.81
反射 シェル解像度: 2.42→2.506 Å / Rmerge(I) obs: 0.4298 / Num. unique obs: 14082 / CC1/2: 0.836

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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: 2.42→49.15 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 32.22 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2678 7065 5 %
Rwork0.225 134207 -
obs0.2271 141272 98.48 %
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: 132.57 Å2 / Biso mean: 55.0677 Å2 / Biso min: 20 Å2
精密化ステップサイクル: final / 解像度: 2.42→49.15 Å
タンパク質核酸リガンド溶媒全体
原子数27256 0 163 547 27966
Biso mean--64.72 48.21 -
残基数----3550
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A10716X-RAY DIFFRACTION4.262TORSIONAL
12B10716X-RAY DIFFRACTION4.262TORSIONAL
13C10716X-RAY DIFFRACTION4.262TORSIONAL
14D10716X-RAY DIFFRACTION4.262TORSIONAL
15E10716X-RAY DIFFRACTION4.262TORSIONAL
16F10716X-RAY DIFFRACTION4.262TORSIONAL
17G10716X-RAY DIFFRACTION4.262TORSIONAL
18H10716X-RAY DIFFRACTION4.262TORSIONAL
19I10716X-RAY DIFFRACTION4.262TORSIONAL
110J10716X-RAY DIFFRACTION4.262TORSIONAL
111K10716X-RAY DIFFRACTION4.262TORSIONAL
112L10716X-RAY DIFFRACTION4.262TORSIONAL
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 (%)
2.42-2.450.39192380.3599450498
2.45-2.480.38032280.339434898
2.48-2.510.38832360.3435449798
2.51-2.540.37792330.3505443098
2.54-2.570.39282340.3391442398
2.57-2.610.41082380.3452451098
2.61-2.640.41982290.3307433998
2.64-2.680.39742360.3276447198
2.68-2.730.35512350.3082445898
2.73-2.770.36132350.2858446498
2.77-2.820.36412320.2864441598
2.82-2.870.29732370.279450998
2.87-2.920.31882360.2702446999
2.92-2.980.35922370.2756450098
2.98-3.050.30582330.2668443798
3.05-3.120.27042340.2512443499
3.12-3.20.32892360.2476450298
3.2-3.280.3012340.2415444999
3.28-3.380.27572370.2328449399
3.38-3.490.27622380.2221453099
3.49-3.610.2572370.2184450099
3.61-3.760.26642330.2031442599
3.76-3.930.24512380.1981452699
3.93-4.140.25032380.1847450599
4.14-4.40.21282380.1782453599
4.4-4.740.20942360.1666447899
4.74-5.210.22122390.1856453499
5.21-5.960.22522390.201454699
5.96-7.510.21032380.1958451799
7.51-100.19562330.1943445996
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)
11.83240.64411.06292.98181.2944.12440.252-0.1531-0.21020.2245-0.09480.1020.5417-0.7674-0.05010.3667-0.0388-0.02830.38880.10720.4331-14.148-4.75836.693
21.3732-0.0738-0.23821.5587-0.42763.1072-0.0188-0.0918-0.0682-0.13030.08070.31440.5165-0.6643-0.15490.4713-0.050.01230.48360.06280.3674-14.376-8.13236.676
31.3678-0.10190.02812.64960.50151.3054-0.2392-0.13460.08570.15860.39350.81720.0692-0.7323-0.08070.3308-0.0152-0.01450.52230.08390.4702-19.214.25137.748
40.9348-0.12650.89110.6124-0.57460.9289-0.2168-0.246-0.04140.12090.06520.0372-0.10960.00930.11650.40620.00270.05480.44820.04670.3695-4.3627.40444.95
53.29221.09981.75392.0876-0.85612.028-0.0541-0.384-0.5311-0.0383-0.2056-0.27790.9461-0.23030.56410.2973-0.0008-0.00260.42070.0290.55067.062-7.66241.148
60.3363-0.91660.45421.8645-0.82251.67320.0064-0.24540.0815-0.2380.0591-0.11780.4255-0.1111-0.08430.5735-0.07740.00940.46140.01160.4239-7.003-9.00124.598
73.79730.4802-1.31132.6557-0.2883.8758-0.02530.2452-0.5326-0.46910.0124-0.4170.45530.52030.16440.48690.0643-0.00150.3547-0.04770.5682.203-15.75329.392
82.11530.90341.68312.25631.98812.70730.09560.0166-0.299-0.0155-0.08810.0330.1449-0.2443-0.01660.339-0.02930.0230.41490.15530.3935-17.226-31.667-14.795
92.0895-1.1872-0.0811.492-0.46322.6796-0.0657-0.012-0.14040.05080.1262-0.02580.1971-0.2838-0.1260.488-0.03320.05790.52380.08710.5882-18.318-34.814-14.73
102.8551-1.90681.85352.65360.64184.41270.28520.4317-0.012-0.08440.10030.7491-0.1168-0.5329-0.19220.44140.00280.15410.62840.11290.6135-25.665-28.034-13.892
110.77771.4189-0.18263.5942-1.57891.4851-0.30340.12030.15470.28580.61370.4303-0.1087-0.8865-0.30110.45830.03310.11480.59910.11020.5219-20.015-20.669-10.669
121.80390.1971.00562.7881-1.03371.6311-0.07170.00290.33230.09360.14440.2132-0.1178-0.2557-0.00470.42520.04280.0560.44760.02750.3996-9.006-14.741-13.889
130.0425-0.05080.66832.1605-0.26980.8379-0.1094-0.2359-0.13730.168-0.00770.00620.0140.10590.11310.4528-0.01260.06520.50090.0390.3737-1.053-26.667-6.914
143.57020.17571.68232.3172-0.17037.6603-0.3508-0.2928-0.50890.2577-0.2415-0.02170.66070.17670.49020.42930.02280.13410.46950.07480.64982.706-40.587-13.601
150.0678-0.18910.05792.8156-0.03730.13950.05420.5860.1707-0.17210.33990.15730.01060.2474-0.04220.5649-0.09130.01040.5630.00940.5909-10.09-38.212-26.205
160.8454-0.83020.88452.7612-1.99132.7225-0.41050.379-0.3812-0.51990.8296-0.0560.7399-0.5843-0.44290.4939-0.0892-0.07750.5030.08680.4757-16.323-37.023-29.351
172.2387-0.4367-0.43912.588-1.21283.94910.13980.0617-0.8906-0.2914-0.2924-0.21450.61660.10280.10530.4963-0.0162-0.04690.3592-0.02190.8149-6.003-46.635-24.448
181.2186-2.1523-0.67893.456-0.22391.41620.09450.1075-0.17260.2109-0.40490.35060.16790.22260.35350.49730.09960.08520.54720.12050.482533.157-22.004-48.666
191.51080.73770.19161.5744-1.16830.8344-0.19640.1309-0.1965-0.43080.0267-0.2530.49470.35130.17530.61920.05620.16280.58040.07630.479533.279-23.843-51.461
200.64831.22880.43191.83860.96472.4775-0.0494-0.19420.0154-0.0308-0.3439-0.4868-0.00150.85310.3150.40980.08570.05120.64920.16720.544740.44-17.213-43.908
211.41170.28040.31570.90070.49391.0774-0.1090.19550.0364-0.09870.0537-0.14830.04820.17940.07020.38150.00280.06350.40750.08750.412724.531-9.845-40.831
222.2122-0.2882-0.60493.249-1.43672.8551-0.2060.43450.22250.05540.3643-0.0944-0.2325-0.66-0.03650.3871-0.02780.0480.5149-0.00790.429512.238-17.661-54.379
230.10040.06310.27750.7418-1.34693.1434-0.20990.1339-0.1311-0.5333-0.2654-0.05530.6450.11380.24880.69410.07940.0770.4983-0.03480.463922.203-34.562-49.483
242.2109-0.61470.88551.00790.08062.9007-0.129-0.01990.0590.08990.04040.297-0.454-0.4772-0.02690.40760.03620.01660.36440.08420.3847-14.6171.068-36.709
250.4616-0.4893-0.75752.58470.10481.7697-0.29050.1046-0.10260.05280.2148-0.00190.0328-0.69180.08610.3901-0.0159-0.00280.55910.08660.5347-19.453-10.013-37.597
260.94960.3127-0.19460.0162-0.60121.1006-0.13110.1994-0.0406-0.23760.1483-0.0390.11860.0238-0.01750.4098-0.02390.00370.42180.06560.3938-4.858-13.574-44.52
270.7657-0.7592-0.14392.2978-0.29172.2328-0.14870.0027-0.02150.25060.1335-0.2931-0.26540.11420.03510.4302-0.0018-0.00460.37220.02350.4788-0.3284.603-32.001
281.3195-0.5046-0.20130.92970.69151.60410.05460.202-0.177-0.10020.0348-0.4829-0.08760.34930.01740.49190.02140.00170.46340.02580.6129-12.21936.541-17.201
292.4853-1.1243-0.18890.8034-1.83413.751-0.08410.14170.0331-0.2667-0.2385-0.8136-0.12270.74070.16090.5019-0.00430.01950.55320.07370.7067-7.23540.649-26.546
301.02740.55410.11261.9834-0.55471.269-0.09760.121-0.1943-0.34920.1176-0.23280.16880.05960.0350.47680.03990.0440.5006-0.04160.5286-23.70537.195-35.076
312.26281.69411.29742.1052-0.25712.70520.11180.0288-0.72040.03090.1047-0.66070.20530.2753-0.15630.45360.01450.01170.48740.02350.5971-26.70325.099-18.012
321.6882-0.37941.2012.7307-0.18371.7529-0.0335-0.3785-0.02860.40910.15220.1802-0.1284-0.4143-0.09160.46790.0364-0.02590.52560.06940.4582-23.30540.058-6.235
331.37751.0979-0.53462.94350.0911.33430.21-0.00080.08460.1733-0.3679-0.7419-0.29540.22190.08440.4018-0.041-0.10530.48930.10830.405833.43916.33748.591
340.95-0.60940.28631.3819-0.73920.5785-0.0318-0.12760.02580.3652-0.1371-0.463-0.28010.28810.14720.4786-0.1099-0.11320.39940.08640.399533.63618.05251.386
350.85860.4712-1.35991.7495-0.7062.74770.34680.53130.52090.049-0.59370.4362-0.37490.85490.06720.3814-0.1629-0.17840.83460.20060.672942.77316.74746.624
360.6799-0.67211.02771.60320.24743.7470.05150.3339-0.18830.0594-0.1176-0.2827-0.39620.8860.14840.3798-0.0254-0.02970.55740.1520.555139.4988.33442.139
370.75340.7940.29311.0609-0.60842.3744-0.07550.22-0.1586-0.06480.1018-0.1275-0.21410.36490.07790.4428-0.04570.00530.51060.05610.407432.2455.47932.086
383.1937-0.60480.95731.1842-1.00352.94880.34730.0690.4131-0.2458-0.3867-0.35760.2541-0.0260.10430.3511-0.01350.04070.37190.03340.518228.7325.78736.044
390.50490.8680.79311.54270.15091.255-0.1163-0.1221-0.0767-0.01850.0160.03230.01480.04540.07420.3654-0.0153-0.01230.36010.10420.340920.8933.10245.242
401.35491.4503-0.8721.1537-0.91712.5491-0.1421-0.1237-0.12110.2685-0.1622-0.015-0.3501-0.15870.21550.51040.0026-0.05680.42180.04290.426420.18721.60649.706
412.22190.9023-0.43842.4689-0.93553.5828-0.2674-0.0957-0.01180.3132-0.0932-0.0207-0.8868-1.09370.29520.66890.0449-0.0460.4142-0.18880.537117.04328.49754.482
422.6437-1.1576-1.59562.60861.48573.91870.13090.05160.17480.0717-0.15640.4423-0.3823-0.64970.12920.32850.009-0.01650.44770.14090.5282-17.06725.94614.775
432.49971.25760.02240.849-0.17252.8907-0.0740.32760.0019-0.38380.05560.16-0.1994-0.4438-0.10680.47510.0266-0.02350.48260.11880.5375-18.17729.11114.813
440.4731-1.17920.05932.2799-0.40950.2366-0.1183-0.1344-0.01040.01240.1627-0.0020.0282-0.3587-0.020.3568-0.0269-0.00890.50630.05390.4508-19.09415.85713.226
450.2721-0.33340.13031.6076-1.09123.03360.02960.11370.0332-0.1270.0032-0.03260.14660.0668-0.05150.3715-0.0108-0.01040.4420.06070.3817-2.83912.7019.089
461.1261-0.8671-0.28920.3267-0.89272.3425-0.06250.04640.340.11050.0843-0.1121-0.36740.0802-0.07850.4526-0.03520.01460.34260.05210.4968-5.5834.33418.426
472.6682-2.014-0.29551.59330.40642.2767-0.07660.4366-0.10250.0287-0.19490.0948-0.02620.40210.31340.3405-0.04650.03030.60680.09810.46135.76419.71210.716
481.5670.42681.23191.7745-0.461.13010.07850.06530.0459-0.1663-0.0919-0.1845-0.1330.36010.04560.4786-0.00330.09560.6070.11120.552636.79918.2197.793
493.3530.43230.70384.2263-0.13222.5936-0.04610.90690.76280.3879-0.3897-0.6428-0.94830.74420.29040.4146-0.1261-0.02330.68830.18880.663944.22422.34113.101
501.31980.4121-1.63321.55661.01052.7377-0.19540.12190.15810.1795-0.697-0.3367-0.9480.19010.54970.4953-0.0404-0.00360.57940.17250.608538.52828.79518.012
510.8397-0.2610.69030.63420.62461.6362-0.00260.2730.1782-0.08790.0086-0.1343-0.27520.07890.0370.4316-0.0777-0.00040.41110.13380.459922.56328.94116.448
523.6071-1.1170.63123.9131-1.24413.94350.17660.4136-0.088-0.6110.10280.23610.4529-0.4373-0.21030.5099-0.05930.06510.66930.00050.523615.65715.8622.665
530.40210.20790.56310.7688-0.95472.7081-0.01260.1483-0.1164-0.1388-0.130.00780.50660.06150.17420.50420.07270.0560.60120.01350.487529.1454.7278.54
541.87091.36340.20711.2438-0.19532.19820.1889-0.29960.1105-0.0803-0.4855-0.128-0.10660.41330.23930.37440.01770.01440.5040.14710.468135.685-25.453-10.743
551.8406-0.528-0.89881.2109-0.97331.9442-0.042-0.2887-0.24170.083-0.31-0.52520.40870.32340.39260.4374-0.009-0.02340.52150.10810.544736.682-23.989-7.938
562.65860.7726-2.07253.9474-0.71433.2015-0.0816-0.5345-0.97710.02-0.8392-0.74870.13360.5410.46520.46740.1664-0.04250.69390.12360.603744.019-27.955-13.187
570.9890.19910.29761.0857-0.09182.5965-0.0721-0.092-0.3957-0.0787-0.0623-0.50550.11390.25850.14930.50290.04380.0490.48170.13750.597133.244-35.272-22.916
581.0050.78840.30331.03180.00171.66720.0198-0.0794-0.13390.0034-0.0324-0.15820.1780.03120.01420.44790.05220.02960.44230.11130.50120.684-34.204-13.89
590.47290.27450.30192.6054-1.50642.4081-0.0276-0.12730.2637-0.09240.25360.64210.0662-0.30840.0790.51210.01460.05170.66680.02210.510515.546-23.69-1.75
600.735-0.1143-0.74111.6991-0.73892.77980.0414-0.1754-0.15590.3574-0.2754-0.1226-0.18650.10510.21690.4209-0.0464-0.04090.52030.05690.392731.992-11.281-12.478
611.9135-0.39020.55982.5253-1.30082.4341-0.2246-0.65190.22090.20980.18740.0361-0.5308-0.71350.17660.50750.0078-0.00710.6645-0.07320.578324.706-9.482-2.891
621.139-0.94650.3121.9721-0.77452.60680.24850.43-0.1357-0.0421-0.09420.4088-0.33010.465-0.16320.5139-0.0258-0.10170.3999-0.07690.624-61.64523.901-34.96
631.2343-0.8193-0.6991.9861-0.56911.31480.09420.01680.0493-0.4718-0.09730.36350.2068-0.2852-0.0340.607-0.0566-0.130.5505-0.10720.5815-61.89722.198-37.848
643.4151-3.03-1.27173.8789-0.06972.39930.3346-0.810.5131-0.35180.20190.36220.1268-0.2155-0.27560.5715-0.1127-0.12970.5979-0.03290.7835-70.4822.735-32.772
650.32810.4196-0.27623.4281.62352.55270.1838-0.31630.2276-0.6673-0.41060.964-0.5016-0.5558-0.0030.4374-0.0226-0.0750.51810.04430.7764-66.50924.764-23.856
661.971-0.42630.48960.96090.09830.6422-0.0761-0.1374-0.28730.0497-0.002-0.0380.17710.02570.06220.51-0.03650.00920.4508-0.00550.5228-51.89729.42-19.151
672.3501-0.6220.52631.4294-0.87921.30150.32220.1265-0.557-0.13820.0907-0.05330.17170.16-0.38990.54330.01830.04260.3998-0.04760.6191-47.10918.897-34.474
682.6616-1.3731.0313.4289-0.14472.70090.04690.3151-0.4231-0.45330.0426-0.18420.1840.2678-0.00420.5548-0.08320.09510.5538-0.04810.518-39.8122.159-37.728
692.7801-0.5413-0.1392.6579-0.19473.2392-0.58660.6614-0.5054-1.15610.58610.5549-0.77291.070.22150.8112-0.1089-0.13480.6596-0.1190.5778-54.91232.587-44.949
701.2517-0.4677-0.93792.6040.38171.19180.18090.73790.2253-0.6786-0.1398-0.3552-0.21440.11010.0350.6829-0.044-0.12770.6417-0.08750.3653-54.22531.105-49.019
712.5297-0.35470.04711.2923-1.12812.9092-0.0957-0.0680.17340.03350.01980.41620.0288-0.24550.07620.43260.03850.00660.4354-0.03690.5665-72.99856.744-18.01
723.078-1.69940.70881.31130.71362.833-0.1837-0.088-0.1673-0.06620.0570.8990.0009-0.63850.01230.4383-0.0041-0.05910.5248-0.01120.7081-74.53353.908-30.173
731.08430.66040.31091.79810.43851.2934-0.09960.07440.3164-0.26560.0940.2394-0.0729-0.05910.02870.48980.0293-0.04990.46410.06430.5503-60.19359.38-32.015
741.33031.0017-0.53062.7996-0.45931.2059-0.004-0.19130.10930.1299-0.0641-0.04490.10380.10740.07510.42880.04140.0310.5046-0.0740.502-57.76359.316-9.562
751.5404-1.4052-1.04220.92621.0062.606-0.04650.41840.1680.03650.0264-0.27720.58370.0375-0.07020.6377-0.05530.10520.52910.05810.7317-21.89870.422-34.95
761.7336-0.33860.76011.3578-0.67141.5365-0.10820.3760.3528-0.34450.0867-0.4144-0.17430.0589-0.01650.5797-0.08010.10240.42960.09730.4946-21.64572.193-37.806
772.4063-1.0397-0.7765.71310.28532.62060.18-0.03780.3505-0.05980.435-0.2616-0.20240.558-0.24190.5913-0.08260.08470.66160.00510.8185-13.05771.625-32.793
781.0572-0.20540.66294.1973-2.21413.25150.1997-0.13450.6763-0.3987-0.0702-0.75670.26540.48880.03310.4956-0.0220.03780.477-0.00950.7233-17.05869.771-24.003
790.65490.69630.15142.013-0.5890.7919-0.22160.04910.21820.09320.0491-0.2968-0.15390.17840.19280.5133-0.0457-0.01890.4623-0.0110.5804-25.59561.505-18.852
800.9473-0.62740.2071.2244-0.35083.7638-0.1289-0.28870.10980.30770.1338-0.0853-0.09230.06650.02310.512900.0020.4083-0.05120.6142-32.40766.816-15.864
812.94290.7471-0.15260.7446-0.57261.0052-0.0708-0.06630.0877-0.0403-0.05590.1209-0.12970.1450.11810.48550.0091-0.02960.30020.05460.5275-38.81372.036-27.83
821.4948-0.68760.13323.26140.25851.9401-0.33350.33790.142-0.22970.18910.5479-0.2224-0.04530.04740.5257-0.106-0.09880.62250.12570.4992-43.74372.309-37.672
832.51990.10520.10563.10150.06632.020.05170.5934-0.1107-0.5826-0.21580.0392-0.0007-0.28750.1550.74530.01310.0820.58290.04290.457-25.09560.963-45.861
841.3226-0.49470.30723.4830.94760.4480.00820.31070.0317-0.78820.4607-0.22790.17580.0351-0.27310.8656-0.05020.00860.85190.13850.5019-35.14265.925-50.914
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:23 )A3 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:55 )A24 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:115 )A56 - 115
4X-RAY DIFFRACTION4( CHAIN A AND RESID 116:229 )A116 - 229
5X-RAY DIFFRACTION5( CHAIN A AND RESID 230:248 )A230 - 248
6X-RAY DIFFRACTION6( CHAIN A AND RESID 249:279 )A249 - 279
7X-RAY DIFFRACTION7( CHAIN A AND RESID 280:298 )A280 - 298
8X-RAY DIFFRACTION8( CHAIN B AND RESID 3:23 )B3 - 23
9X-RAY DIFFRACTION9( CHAIN B AND RESID 24:55 )B24 - 55
10X-RAY DIFFRACTION10( CHAIN B AND RESID 56:70 )B56 - 70
11X-RAY DIFFRACTION11( CHAIN B AND RESID 71:99 )B71 - 99
12X-RAY DIFFRACTION12( CHAIN B AND RESID 100:148 )B100 - 148
13X-RAY DIFFRACTION13( CHAIN B AND RESID 149:229 )B149 - 229
14X-RAY DIFFRACTION14( CHAIN B AND RESID 230:248 )B230 - 248
15X-RAY DIFFRACTION15( CHAIN B AND RESID 249:262 )B249 - 262
16X-RAY DIFFRACTION16( CHAIN B AND RESID 263:279 )B263 - 279
17X-RAY DIFFRACTION17( CHAIN B AND RESID 280:298 )B280 - 298
18X-RAY DIFFRACTION18( CHAIN C AND RESID 3:23 )C3 - 23
19X-RAY DIFFRACTION19( CHAIN C AND RESID 24:55 )C24 - 55
20X-RAY DIFFRACTION20( CHAIN C AND RESID 56:98 )C56 - 98
21X-RAY DIFFRACTION21( CHAIN C AND RESID 99:226 )C99 - 226
22X-RAY DIFFRACTION22( CHAIN C AND RESID 227:248 )C227 - 248
23X-RAY DIFFRACTION23( CHAIN C AND RESID 249:298 )C249 - 298
24X-RAY DIFFRACTION24( CHAIN D AND RESID 3:55 )D3 - 55
25X-RAY DIFFRACTION25( CHAIN D AND RESID 56:115 )D56 - 115
26X-RAY DIFFRACTION26( CHAIN D AND RESID 116:226 )D116 - 226
27X-RAY DIFFRACTION27( CHAIN D AND RESID 227:298 )D227 - 298
28X-RAY DIFFRACTION28( CHAIN E AND RESID 5:55 )E5 - 55
29X-RAY DIFFRACTION29( CHAIN E AND RESID 56:99 )E56 - 99
30X-RAY DIFFRACTION30( CHAIN E AND RESID 100:200 )E100 - 200
31X-RAY DIFFRACTION31( CHAIN E AND RESID 201:248 )E201 - 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 56:69 )F56 - 69
36X-RAY DIFFRACTION36( CHAIN F AND RESID 70:98 )F70 - 98
37X-RAY DIFFRACTION37( CHAIN F AND RESID 99:127 )F99 - 127
38X-RAY DIFFRACTION38( CHAIN F AND RESID 128:148 )F128 - 148
39X-RAY DIFFRACTION39( CHAIN F AND RESID 149:226 )F149 - 226
40X-RAY DIFFRACTION40( CHAIN F AND RESID 227:279 )F227 - 279
41X-RAY DIFFRACTION41( CHAIN F AND RESID 280:298 )F280 - 298
42X-RAY DIFFRACTION42( CHAIN G AND RESID 3:23 )G3 - 23
43X-RAY DIFFRACTION43( CHAIN G AND RESID 24:55 )G24 - 55
44X-RAY DIFFRACTION44( CHAIN G AND RESID 56:115 )G56 - 115
45X-RAY DIFFRACTION45( CHAIN G AND RESID 116:200 )G116 - 200
46X-RAY DIFFRACTION46( CHAIN G AND RESID 201:298 )G201 - 298
47X-RAY DIFFRACTION47( CHAIN H AND RESID 3:23 )H3 - 23
48X-RAY DIFFRACTION48( CHAIN H AND RESID 24:55 )H24 - 55
49X-RAY DIFFRACTION49( CHAIN H AND RESID 56:70 )H56 - 70
50X-RAY DIFFRACTION50( CHAIN H AND RESID 71:99 )H71 - 99
51X-RAY DIFFRACTION51( CHAIN H AND RESID 100:229 )H100 - 229
52X-RAY DIFFRACTION52( CHAIN H AND RESID 230:248 )H230 - 248
53X-RAY DIFFRACTION53( CHAIN H AND RESID 249:298 )H249 - 298
54X-RAY DIFFRACTION54( CHAIN I AND RESID 3:23 )I3 - 23
55X-RAY DIFFRACTION55( CHAIN I AND RESID 24:55 )I24 - 55
56X-RAY DIFFRACTION56( CHAIN I AND RESID 56:70 )I56 - 70
57X-RAY DIFFRACTION57( CHAIN I AND RESID 71:129 )I71 - 129
58X-RAY DIFFRACTION58( CHAIN I AND RESID 130:226 )I130 - 226
59X-RAY DIFFRACTION59( CHAIN I AND RESID 227:248 )I227 - 248
60X-RAY DIFFRACTION60( CHAIN I AND RESID 249:279 )I249 - 279
61X-RAY DIFFRACTION61( CHAIN I AND RESID 280:298 )I280 - 298
62X-RAY DIFFRACTION62( CHAIN J AND RESID 3:23 )J3 - 23
63X-RAY DIFFRACTION63( CHAIN J AND RESID 24:55 )J24 - 55
64X-RAY DIFFRACTION64( CHAIN J AND RESID 56:70 )J56 - 70
65X-RAY DIFFRACTION65( CHAIN J AND RESID 71:99 )J71 - 99
66X-RAY DIFFRACTION66( CHAIN J AND RESID 100:200 )J100 - 200
67X-RAY DIFFRACTION67( CHAIN J AND RESID 201:226 )J201 - 226
68X-RAY DIFFRACTION68( CHAIN J AND RESID 227:248 )J227 - 248
69X-RAY DIFFRACTION69( CHAIN J AND RESID 249:262 )J249 - 262
70X-RAY DIFFRACTION70( CHAIN J AND RESID 263:298 )J263 - 298
71X-RAY DIFFRACTION71( CHAIN K AND RESID 3:70 )K3 - 70
72X-RAY DIFFRACTION72( CHAIN K AND RESID 71:98 )K71 - 98
73X-RAY DIFFRACTION73( CHAIN K AND RESID 99:226 )K99 - 226
74X-RAY DIFFRACTION74( CHAIN K AND RESID 227:298 )K227 - 298
75X-RAY DIFFRACTION75( CHAIN L AND RESID 3:23 )L3 - 23
76X-RAY DIFFRACTION76( CHAIN L AND RESID 24:55 )L24 - 55
77X-RAY DIFFRACTION77( CHAIN L AND RESID 56:70 )L56 - 70
78X-RAY DIFFRACTION78( CHAIN L AND RESID 71:99 )L71 - 99
79X-RAY DIFFRACTION79( CHAIN L AND RESID 100:148 )L100 - 148
80X-RAY DIFFRACTION80( CHAIN L AND RESID 149:171 )L149 - 171
81X-RAY DIFFRACTION81( CHAIN L AND RESID 172:226 )L172 - 226
82X-RAY DIFFRACTION82( CHAIN L AND RESID 227:248 )L227 - 248
83X-RAY DIFFRACTION83( CHAIN L AND RESID 249:279 )L249 - 279
84X-RAY DIFFRACTION84( CHAIN L AND RESID 280:298 )L280 - 298

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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://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