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- PDB-8qzi: Crystal structure of PptT-ACP from Mycobacterium tuberculosis -

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基本情報

登録情報
データベース: PDB / ID: 8qzi
タイトルCrystal structure of PptT-ACP from Mycobacterium tuberculosis
要素
  • 4'-phosphopantetheinyl transferase PptT
  • Phenolphthiocerol/phthiocerol polyketide synthase subunit C
キーワードTRANSFERASE
機能・相同性
機能・相同性情報


(phenol)carboxyphthiodiolenone synthase / siderophore metabolic process / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / enterobactin synthetase complex / holo-[acyl-carrier-protein] synthase / enterobactin biosynthetic process / siderophore biosynthetic process ...(phenol)carboxyphthiodiolenone synthase / siderophore metabolic process / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / Actinobacterium-type cell wall biogenesis / enterobactin synthetase complex / holo-[acyl-carrier-protein] synthase / enterobactin biosynthetic process / siderophore biosynthetic process / holo-[acyl-carrier-protein] synthase activity / DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / magnesium ion binding / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
Enterobactin synthetase-like, component D / 4'-phosphopantetheinyl transferase, N-terminal domain / 4'-phosphopantetheinyl transferase N-terminal domain / Zinc-binding dehydrogenase / : / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / : / Polyketide synthase dehydratase domain ...Enterobactin synthetase-like, component D / 4'-phosphopantetheinyl transferase, N-terminal domain / 4'-phosphopantetheinyl transferase N-terminal domain / Zinc-binding dehydrogenase / : / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
COENZYME A / ISOPROPYL ALCOHOL / : / 4'-phosphopantetheinyl transferase PptT / Phenolphthiocerol/phthiocerol polyketide synthase subunit C
類似検索 - 構成要素
生物種Mycobacterium tuberculosis (結核菌)
Mycobacterium tuberculosis H37Rv (結核菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å
データ登録者Gavalda, S. / Mourey, L. / Pedelacq, J.D.
資金援助 フランス, 1件
組織認可番号国
Agence Nationale de la Recherche (ANR)09-BLAN-0298-01 フランス
引用ジャーナル: Acs Catalysis / 年: 2024
タイトル: Catalytic Cycle of Type II 4'-Phosphopantetheinyl Transferases
著者: Gavalda, S. / Faille, A. / Fioccola, S. / Nguyen, M.C. / Carivenc, C. / Rottier, K. / Rufin, Y. / Saitta, S. / Czaplicki, G. / Guilhot, C. / Chalut, C. / Brut, M. / Mourey, L. / Pedelacq, J.D.
履歴
登録2023年10月27日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年6月19日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: 4'-phosphopantetheinyl transferase PptT
B: 4'-phosphopantetheinyl transferase PptT
C: 4'-phosphopantetheinyl transferase PptT
D: 4'-phosphopantetheinyl transferase PptT
E: Phenolphthiocerol/phthiocerol polyketide synthase subunit C
F: Phenolphthiocerol/phthiocerol polyketide synthase subunit C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)148,40320
ポリマ－144,7736
非ポリマー3,63014
水90150
1
A: 4'-phosphopantetheinyl transferase PptT
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)27,7864
ポリマ－26,9091
非ポリマー8773
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-16 kcal/mol
Surface area10450 Å2
手法PISA
2
B: 4'-phosphopantetheinyl transferase PptT
F: Phenolphthiocerol/phthiocerol polyketide synthase subunit C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,3555
ポリマ－45,4782
非ポリマー8773
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-25 kcal/mol
Surface area14860 Å2
手法PISA
3
C: 4'-phosphopantetheinyl transferase PptT
E: Phenolphthiocerol/phthiocerol polyketide synthase subunit C
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,4757
ポリマ－45,4782
非ポリマー9985
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-25 kcal/mol
Surface area14060 Å2
手法PISA
4
D: 4'-phosphopantetheinyl transferase PptT
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)27,7864
ポリマ－26,9091
非ポリマー8773
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-16 kcal/mol
Surface area10790 Å2
手法PISA
単位格子
Length a, b, c (Å)47.335, 280.843, 47.340
Angle α, β, γ (deg.)90.000, 92.829, 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

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要素

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タンパク質 , 2種, 6分子 ABCDEF

#1: タンパク質
4'-phosphopantetheinyl transferase PptT


分子量: 26908.865 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis (結核菌)
遺伝子: pptT / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: O33336
#2: タンパク質 Phenolphthiocerol/phthiocerol polyketide synthase subunit C / (Phenol)carboxyphthiodiolenone synthase subunit C / Beta-ketoacyl-acyl-carrier-protein synthase I / ...(Phenol)carboxyphthiodiolenone synthase subunit C / Beta-ketoacyl-acyl-carrier-protein synthase I / Phthiocerol synthesis polyketide synthase type I PpsC


分子量: 18568.777 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis H37Rv (結核菌)
株: ATCC 25618 / H37Rv / 遺伝子: ppsC, Rv2933 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P96202, (phenol)carboxyphthiodiolenone synthase

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非ポリマー , 4種, 64分子

#3: 化合物
ChemComp-COA / COENZYME A / CoA


分子量: 767.534 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C21H36N7O16P3S / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 8 / 由来タイプ: 天然 / 式: Mn / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物 ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / 2-プロパノ-ル


分子量: 60.095 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O / タイプ: SUBJECT OF INVESTIGATION / コメント: alkaloid*YM
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 50 / 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: 49.19 %
結晶化温度: 285 K / 手法: 蒸気拡散法 / pH: 7.25 / 詳細: 0.1 M Hepes 5 % isopropanol 24 % PEG4000

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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: 0.9791 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2015年2月5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: 0.9791 Å / 相対比: 1
反射解像度: 2.5→47.28 Å / Num. obs: 42194 / % possible obs: 99.6 % / 冗長度: 3.7 % / Biso Wilson estimate: 60.25 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.3
反射 シェル解像度: 2.5→2.59 Å / Num. unique obs: 4122 / CC1/2: 0.555

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解析

ソフトウェア
名称バージョン分類
autoPROCdata processing
XDSデータ削減
Cootモデル構築
PHASER位相決定
PHENIX1.17.1-3660精密化
精密化構造決定の手法: 分子置換 / 解像度: 2.5→47.28 Å / SU ML: 0.4619 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 27.7444
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2409 3850 4.71 %
Rwork0.1957 77957 -
obs0.1978 42180 97.14 %
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: 60.2 Å2
精密化ステップサイクル: LAST / 解像度: 2.5→47.28 Å
タンパク質核酸リガンド溶媒全体
原子数8184 0 149 50 8383
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00828541
X-RAY DIFFRACTIONf_angle_d1.036311702
X-RAY DIFFRACTIONf_chiral_restr0.05271343
X-RAY DIFFRACTIONf_plane_restr0.00751492
X-RAY DIFFRACTIONf_dihedral_angle_d22.82393070
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.5041980.4342681X-RAY DIFFRACTION90.91
2.53-2.560.37031630.39282879X-RAY DIFFRACTION98.45
2.56-2.60.40361490.36822957X-RAY DIFFRACTION98.23
2.6-2.640.32041300.34873001X-RAY DIFFRACTION98.21
2.64-2.680.38071300.3112767X-RAY DIFFRACTION98.57
2.68-2.720.37271820.29992983X-RAY DIFFRACTION98.78
2.72-2.760.28891290.27773006X-RAY DIFFRACTION98.99
2.76-2.810.3371710.2752881X-RAY DIFFRACTION98.64
2.81-2.860.28841190.272927X-RAY DIFFRACTION98.8
2.86-2.920.30361570.24422928X-RAY DIFFRACTION98.69
2.92-2.980.29051620.23673043X-RAY DIFFRACTION98.77
2.98-3.040.31331530.24892787X-RAY DIFFRACTION98.72
3.04-3.110.30151460.233020X-RAY DIFFRACTION98.63
3.11-3.190.26591570.24312839X-RAY DIFFRACTION97.88
3.19-3.280.29651390.21152985X-RAY DIFFRACTION98.27
3.28-3.370.27251560.20812942X-RAY DIFFRACTION97.91
3.37-3.480.25341130.20742846X-RAY DIFFRACTION97.62
3.48-3.60.22861520.18352979X-RAY DIFFRACTION97.3
3.6-3.750.23081420.1892760X-RAY DIFFRACTION96.89
3.75-3.920.22431350.16612924X-RAY DIFFRACTION96.77
3.92-4.130.21941290.16322846X-RAY DIFFRACTION96.56
4.13-4.380.17811500.14732886X-RAY DIFFRACTION96.29
4.38-4.720.21741290.15012939X-RAY DIFFRACTION95.67
4.72-5.20.21831240.16012818X-RAY DIFFRACTION95.12
5.2-5.950.19981460.17412828X-RAY DIFFRACTION95.38
5.95-7.490.24241490.17532766X-RAY DIFFRACTION95.01
7.49-47.280.17131400.15422739X-RAY DIFFRACTION91.54
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)
15.66499867463.68986952852-3.071775842354.528275800981.309898649346.84718262802-0.729369026942-0.2447219831761.287200650840.04608684394290.06480652778880.641856890235-1.49844279149-1.139027920120.5295017543681.084042211080.36337129587-0.05455343007970.524532364274-0.1244212831440.511144236389-32.649912498986.543055805340.138027835
22.519171487070.5307784936380.7814029301920.8333068630440.3078980852551.72105825648-0.235113566421-1.51184532086-0.6982223517950.977541497130.1138379362910.1595775924070.5916325540130.07396517903220.2010789758861.557745694350.3634259346950.3333776055280.9706303802140.2631007685120.414185466488-29.043855143767.911976867454.2649165252
36.02689418396-2.21369042699-2.05321900843.199885479981.900471870725.54269942611-0.705830248769-0.609426739771-0.5990898213330.5830924353030.3062658144760.6712108421890.219116876124-1.050161430320.4090113823681.147959170310.204456753710.2740225924650.845443893004-0.03074619531770.418768488337-34.505452034371.448935282646.8783705324
47.43980795718-0.0168209111491-0.3145801254724.300208092961.751067861996.88164066246-0.3093183740490.176499666208-0.285629349453-0.2463354952750.0219059147773-0.0680618701045-0.267612609318-0.3485259957320.3359579422790.9163774632070.226737846202-0.01362433196490.385444704664-0.04999770007960.248317589843-24.90387424275.272074178135.635579221
55.96426704774-1.436710538472.13734930813.7568720592.145119483652.84487748114-0.5017996798421.868645503140.361035733683-2.445237949-0.197228927776-1.2423778393-1.382835622441.125915014730.3566405617371.64782896352-0.2278984051290.404960752831.067838141250.112102226760.799742245208-12.060339059381.685611365624.8800852619
65.14810922566-0.2159329708380.1713042946932.70241056736-0.1124090639045.11883139328-0.08428247993920.9364895368570.008333923815-0.865982659356-0.158408149513-0.00777488968818-0.38029251078-0.5622851951310.2076504195151.119820944460.2401192676650.03838371928020.655250280939-0.08334126580410.307231586544-25.790293261876.580526598427.8445221901
76.06743497764-3.34340589211-0.1688551153315.46789076286-2.036602965112.302177173720.7966909417661.07270032126-1.25170365365-0.78374001909-0.0004565583062460.6877612864860.7998722834260.5055532095490.5802561195440.4813641405360.360508339634-0.07234849389980.461857247304-0.7305114323491.41234391632-7.8305733135517.730690770516.8482174158
85.41798958905-1.10622272077-1.446510690822.973190379310.3753674993026.934882017360.2469821823970.7178197701840.34440418106-0.501326812260.158550550964-0.977887379044-0.7111408015820.806713023831-0.2594945560.3766477523870.004783601262490.1545441480630.672405259748-0.3058538291351.05092629071-0.37294122447432.721426336617.4724255666
93.64355948625-1.954807784344.205383889396.03198246727-2.310785213544.83099745658-0.6609964378830.2578938456770.187226588522-0.904099502348-0.7142348401650.281791058296-1.17126852308-1.768331939881.298774489570.379029505710.11180763209-0.06124616691590.674532993235-0.2491942856590.758470268946-13.572400987627.342738143816.0114323831
105.128322295890.8924767443115.780343284319.029738590762.94089439848.754549189250.0249754730652-1.908965381521.301575577921.838669879480.4090723006760.680340369794-0.207424009517-1.46336062641-0.2265077606080.7079777837750.1342361506580.2703541237070.624199680341-0.1524211230420.916399709805-18.731838745932.270427188437.6089809927
114.576124981061.263168246193.665215353530.5499748305090.9370420005133.019427694410.254617878424-1.73823900782-1.828484698311.127863773580.5102245590721.549574634530.794702240485-1.98476293174-0.65176011780.874011981186-0.1248091648960.3087567984851.037705719950.1948174475151.61578458886-24.992100903323.54996347336.3796309252
125.06496117837-0.3930735133441.186345260033.85186969131-0.1971201535776.920232391310.1026361350270.439108169232-0.567685458915-0.151157716996-0.1903722268260.8365003382770.202486331891-1.070832196580.005712743092520.3026448593840.0614504781802-0.02076762341550.593439251427-0.238105377711.0047515566-20.594086069227.790450904723.00802597
134.717369392770.2906954580810.5876540313124.59565358579-0.7566250523215.244057659980.118824856413-1.072231836781.423177946370.653983015481-0.1244220285990.244657908056-1.12779049602-0.1941078618150.362649140230.559788824982-0.054553539359-0.09677452104570.711444326104-0.7356391266951.7001185273415.229706096917.69230427717.92642994616
143.012234968772.88049278553-1.214367302792.81961686947-0.8476937978735.304600605450.2292930021750.185768499120.8396734060310.133226988882-0.16491930228-1.294481146970.5022849040760.865640809241-0.05582571224430.308636678770.114136837799-0.06062388187060.8728831002020.1436263956461.5329739641329.385272779-1.12679691294.2139490001
151.989441772040.9782684686020.2277439382466.645534674553.913988407215.84056543033-0.568963063169-0.8522436605870.9276223113710.07236336195620.254524034364-0.533105521409-0.3536524061340.08030249521610.2668592832220.3789667886090.148645120154-0.1858851885560.845985173842-0.3608272951541.1412223943425.39390764024.347740050795.92493824308
166.27409215264-1.819537208560.8699056272285.71344892059-0.6932318383561.19623999341-0.381730591199-2.457445723390.2497308726360.6414080143210.449146349024-0.3442905910410.0490354002497-0.189737293115-0.01843186126740.3660145203560.167799102064-0.03479176586911.17729665314-0.2724358958130.83368923340916.19444562274.7219929910.533483971
179.64875413694.08027530582-0.192436285761.99951284964-1.137024611712.329306513670.1003396906521.41900111804-0.457050436593-1.971651680950.1774495485270.1491026949920.794586719655-0.165575839974-0.2183173284260.770363289530.14991355385-0.3540692317250.338882206668-0.3248188802191.190677013045.303578838431.98585973112-12.6478116031
188.27383881241-0.7735898816650.4170909333473.90995054846-0.7768492881073.294469755170.264945498094-0.475469456246-0.163700526821-0.614371149437-0.07263414244720.8913515554040.390836475076-0.263540661119-0.1219234817150.3735988771510.00573168647735-0.09099078266570.383133656316-0.2002810464080.9138859218671.508090906096.13613446079-3.91618570588
194.27162323313-1.04252242673-1.390550627189.36572237566-5.298865178978.92242330548-0.0548798012986-1.25951980053-1.16718682881-0.5180385675960.4047002250361.316818841750.149712488394-0.568329392796-0.3573342578520.346691371288-0.0808319835404-0.01559224631610.86996866059-0.01576342075941.30269717993-0.9104927834362.419888710041.64707894232
203.26719033498-0.485120249517-0.4171655767536.5788870453-2.900535430453.73648230348-0.298535246269-0.4714599005750.775315051503-0.2923322299740.1834952416970.260944628029-0.223694724118-0.3601852812150.1357435441350.4075188490080.0455343900557-0.05676942821920.49666054706-0.2340454357011.360673566991.127031282715.9750552301-1.08414190334
212.01984089976-1.34308684192-1.448284426022.920463144552.04372252113.08560799039-0.299480661911-2.11978460396-0.8756816435040.6320692788291.03332259110.05868072510550.370578492243-0.187856852623-0.3594336048570.5609200305290.2528412578030.2684085197071.463918473150.23551965041.79149490921-3.20591398050.17176321428214.4281476108
229.36984702929-3.96580473530.9575924612255.57797271719-0.8568742079458.427837460090.0915316075719-1.279396381520.923708121233-0.0332306042440.3098767536080.0074986115881-0.4531182657850.251003141789-0.296279022330.234611238971-0.0169176139620.07581670333570.550726202043-0.3177360219440.9290574036497.0511783925513.28739926251.32265119319
236.25901044979-5.447960165554.863229299164.84020220641-3.545757741318.70737127055-0.474053767125-1.08414096086-1.367467404430.1991084689920.852970712330.7483910479281.20487999299-2.06848506582-0.1508841620681.64220685652-0.490667579489-0.04204312506060.842677192210.1128986900380.533931393016-6.8290829368-53.8979472079-15.4017917903
244.44625188252-2.725380537881.324771237322.239866721431.007506633046.03678221973-0.1287943139180.768145586920.291677696293-1.317601038560.183853140119-0.01760684739210.126457094272-0.357314116423-0.03541575878881.45597200212-0.09453243220950.0113305819670.8949813822440.1660577109920.399019548702-3.02739529676-34.700291488-29.5778814848
251.59768774744-0.493371940590.4753739249251.59383123-0.481870873464.801873158270.1710272573110.7949959276740.0368192074256-0.7659787112180.5505483031780.2892293176011.03302252578-1.107322954290.6272365410641.35926385205-0.484236014038-0.1656134093361.05806412690.2276622298580.181005045166-7.57676968194-39.9619662158-25.1648396356
267.462457936985.233124784865.243677840775.029998963034.347664234754.437901855540.135609524376-0.7890118120430.196083421894-0.3130655707050.005421974018381.67095176105-1.22383981278-2.76598769299-0.1668050582031.101075548510.0477804766843-0.1454214810931.679310803390.2458512830330.567050221774-13.4566076092-34.1472018365-16.1064154074
272.14502188017-0.660761995680.8481774006315.02861039482-2.225191121797.84140676731-0.221682506009-0.1718500333630.2486418204780.5314886016360.0492796395741-0.343307964653-0.108691888926-0.9161401171270.09631270362050.847309802054-0.1666677684420.007313230735330.4576328809540.01108374751760.3061114768862.148162527-43.2120943942-7.17897430239
284.62840781394-0.918397071848-0.7340868328874.74094322225-1.38041023746.329387158720.12999490207-0.2880678879310.1643647017120.9764308369360.0641404503883-0.338811596035-0.214894280507-1.18460284556-0.2539696164411.01710606816-0.102785885871-0.02176988057210.662107490627-0.01381100724530.274995082964-0.230083719667-41.1680210081-2.76535181421
293.99229752337-1.11606189541-2.841945435942.499721642253.025162891037.292172265410.472823554825-0.6280612086950.317432737635-0.06911972712140.1052383088710.583590031821-0.951587677326-1.83604907966-0.5674032386061.405552243520.07232051548980.1802106411571.1743613850.1491295163030.355882129918-9.40309935708-41.17001899711.84649564023
307.88342747723-0.450732361134-0.7843454646343.47809000812-2.9829588947.04781939158-0.1156358627220.257643666754-0.3695788674550.2801715649210.1159173100690.07580325879580.975153905948-0.8566442696820.3072947395151.26087825878-0.4264150406860.1554323725880.538961134018-0.09041185884860.240865047646-0.667602687615-49.4944183119-7.53476455506
312.11134904798-2.39645546241-1.81910024145.34588785477-1.256586551955.774364046590.219452662221-0.2207317019630.77518841668-1.15232611896-0.0828601148342-1.856335428710.1350631476690.323347133569-0.3352868731820.997737245965-0.0123866456169-0.006157529481110.53520874420.007389698880211.5063074082810.9315867327-22.9442580422-14.7895991009
328.74912860824-2.438556174523.377457845513.61040772513-5.512076916488.435061625230.19422187028-1.34854540097-0.65032994392-0.945627490599-0.52039377846-0.5659474382170.8152957147330.8443623772250.2058491365891.18895475640.0376107250723-0.2958238859061.01914191881-0.006790301734291.3500166857321.2069575347-13.2878682269-6.13161798661
337.99416534936-4.61299432371-0.2944784151415.29343998985.020534830098.941400999430.468525583258-0.0793050116574-0.990218923318-0.6595456008690.0818212180888-0.08163485808410.4185995777490.158827453518-0.5638910580961.146843119860.0523564610901-0.2929814444750.622414835751-0.01895944298411.244406416388.19132443209-10.0006183992-11.3745848163
348.859494309057.796816332066.162579556547.211394640156.05407743855.420541473590.630236813818-0.414951211929-1.2206352253-1.66515063673-2.039141364710.8200490085151.3429468164-0.9442640735051.192938655492.26254626382-0.0418367722971-0.4389510634210.751423285452-0.09581259167151.629161901241.12263815118-14.3077260624-7.93290502601
359.44987463375-5.30501743266-7.009580763473.116148533554.271070282796.015082986470.106769803521-4.18703060368-0.9505442225160.6611172463271.782783347560.6346461885221.28766769830.114067598923-1.8563016160.7852843704910.138942844696-0.2199557432131.32067247352-0.01065825702022.831889136739.71112022995-14.13626688060.0374344865405
367.856547094615.120555946.399280105674.26397589923.417836916877.233363013731.43645873362-0.688419119546-1.743405899781.25313618551-0.514913746645-1.025867063243.42384150452-1.47564089032-0.9116632297441.95329874692-0.191826766153-0.06077445863890.7642049860520.02322709618331.115207342436.81207370042-23.2145144808-5.79955774899
377.48121644876-1.354878697241.695243158347.09048305334-3.168902842125.24212807697-0.51762581612-0.126587532591-1.582570341172.430034136361.73933199179-0.6049785917680.3212226397660.391099216367-0.8875204214031.912996984760.208097255385-0.02091808386270.825805956606-0.2587941698121.32388863247-10.899357269154.20644617141.929282883
386.601677268855.62071445465-3.216656893375.31354134314-2.722088437931.58091372310.1486273320041.33809518166-1.168001249050.775092300145-0.0874722410584-1.74164839556-0.5210744655260.182102393081-0.07548780421061.053365183410.1231357320770.1865072616261.02772423106-0.2541446208721.65443084167-5.6783703338145.576997193831.2562730386
392.68589542162.103511316221.216277718859.29869779166-3.547456373263.19210036752-0.271666172511.08592914736-0.5353339562770.6775417275630.346032669360.9455247355080.16538781958-0.497691374652-0.172577878051.220461622310.190593412730.4147257501271.03919847003-0.2609651722521.64051253417-16.1741425749.454720112332.8789630458
404.611628245513.829005489260.0931358013035.81236649775-4.219666987837.00917620680.218808205706-0.5334864145862.364703631012.466676978360.3637922808053.06944291358-2.56084609837-2.30646071734-0.6244985585222.05874451920.5424586141640.2744703945161.027645681420.1040887074861.70041051149-20.145123176358.760554319933.3957391383
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 133 )
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 147 )
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 227 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 24 )
8X-RAY DIFFRACTION8chain 'B' and (resid 25 through 104 )
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 117 )
10X-RAY DIFFRACTION10chain 'B' and (resid 118 through 131 )
11X-RAY DIFFRACTION11chain 'B' and (resid 132 through 147 )
12X-RAY DIFFRACTION12chain 'B' and (resid 148 through 227 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 24 )
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 45 )
15X-RAY DIFFRACTION15chain 'C' and (resid 46 through 65 )
16X-RAY DIFFRACTION16chain 'C' and (resid 66 through 117 )
17X-RAY DIFFRACTION17chain 'C' and (resid 118 through 129 )
18X-RAY DIFFRACTION18chain 'C' and (resid 130 through 167 )
19X-RAY DIFFRACTION19chain 'C' and (resid 168 through 182 )
20X-RAY DIFFRACTION20chain 'C' and (resid 183 through 195 )
21X-RAY DIFFRACTION21chain 'C' and (resid 196 through 208 )
22X-RAY DIFFRACTION22chain 'C' and (resid 209 through 227 )
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 24 )
24X-RAY DIFFRACTION24chain 'D' and (resid 25 through 45 )
25X-RAY DIFFRACTION25chain 'D' and (resid 46 through 76 )
26X-RAY DIFFRACTION26chain 'D' and (resid 77 through 86 )
27X-RAY DIFFRACTION27chain 'D' and (resid 87 through 147 )
28X-RAY DIFFRACTION28chain 'D' and (resid 148 through 187 )
29X-RAY DIFFRACTION29chain 'D' and (resid 188 through 208 )
30X-RAY DIFFRACTION30chain 'D' and (resid 209 through 227 )
31X-RAY DIFFRACTION31chain 'E' and (resid 2061 through 2085 )
32X-RAY DIFFRACTION32chain 'E' and (resid 2086 through 2104 )
33X-RAY DIFFRACTION33chain 'E' and (resid 2105 through 2119 )
34X-RAY DIFFRACTION34chain 'E' and (resid 2120 through 2126 )
35X-RAY DIFFRACTION35chain 'E' and (resid 2127 through 2133 )
36X-RAY DIFFRACTION36chain 'E' and (resid 2134 through 2146 )
37X-RAY DIFFRACTION37chain 'F' and (resid 2058 through 2091 )
38X-RAY DIFFRACTION38chain 'F' and (resid 2092 through 2110 )
39X-RAY DIFFRACTION39chain 'F' and (resid 2111 through 2138 )
40X-RAY DIFFRACTION40chain 'F' and (resid 2139 through 2145 )

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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