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- PDB-4fox: Crystal Structure of Mtb ThyA in complex with dUMP and Raltitrexed -

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基本情報

登録情報
データベース: PDB / ID: 4fox
タイトルCrystal Structure of Mtb ThyA in complex with dUMP and Raltitrexed
要素Thymidylate synthase
キーワードTRANSFERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / thymidylate synthase
機能・相同性
機能・相同性情報


dUMP catabolic process / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / response to antibiotic / cytosol / cytoplasm
類似検索 - 分子機能
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
TOMUDEX / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase ThyA
類似検索 - 構成要素
生物種Mycobacterium tuberculosis (結核菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å
データ登録者Reddy, M.C.M. / Bruning, J.B. / Sacchettini, J.C. / Harshbarger, W. / TB Structural Genomics Consortium (TBSGC)
引用ジャーナル: To be Published
タイトル: Crystal structure of binary and ternary complexes of thymidylate synthase (ThyA) from Mycobacterium tuberculosis: Insights into the selectivity and mode of inhibition
著者: Reddy, M.C.M. / Bruning, J.B. / Sacchettini, J.C. / Harshbarger, W.
履歴
登録2012年6月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年8月7日Provider: repository / タイプ: Initial release
改定 1.12023年9月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Thymidylate synthase
B: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
E: Thymidylate synthase
F: Thymidylate synthase
G: Thymidylate synthase
H: Thymidylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)245,21224
ポリマ-239,0798
非ポリマー6,13316
6,341352
1
A: Thymidylate synthase
B: Thymidylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,3036
ポリマ-59,7702
非ポリマー1,5334
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-14 kcal/mol
Surface area20500 Å2
手法PISA
2
C: Thymidylate synthase
D: Thymidylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,3036
ポリマ-59,7702
非ポリマー1,5334
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-18 kcal/mol
Surface area20240 Å2
手法PISA
3
E: Thymidylate synthase
F: Thymidylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,3036
ポリマ-59,7702
非ポリマー1,5334
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-16 kcal/mol
Surface area19970 Å2
手法PISA
4
G: Thymidylate synthase
H: Thymidylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,3036
ポリマ-59,7702
非ポリマー1,5334
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-14 kcal/mol
Surface area20140 Å2
手法PISA
単位格子
Length a, b, c (Å)91.342, 138.444, 99.948
Angle α, β, γ (deg.)90.000, 107.000, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Thymidylate synthase / TS / TSase


分子量: 29884.830 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis (結核菌)
: H37Rv / 遺伝子: MT2834, MTV002.29c, Rv2764c, thyA / プラスミド: pET28 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: P67044, UniProt: P9WFR9*PLUS, thymidylate synthase
#2: 化合物
ChemComp-D16 / TOMUDEX / ZD1694 / Raltitrexed / ラルチトレキセド


分子量: 458.488 Da / 分子数: 8 / 由来タイプ: 合成 / : C21H22N4O6S / コメント: 化学療法薬, 阻害剤*YM
#3: 化合物
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / dUMP


分子量: 308.182 Da / 分子数: 8 / 由来タイプ: 合成 / : C9H13N2O8P
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 352 / 由来タイプ: 天然 / : H2O

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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: 2.53 Å3/Da / 溶媒含有率: 51.34 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.4
詳細: 2M ammonium sulfate, 0.1M imidazole 6.4, 5mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-B / 波長: 0.91924 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2010年2月10日 / 詳細: mirrors
放射モノクロメーター: Double crystal cryo-cooled Si(111)
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: 0.91924 Å / 相対比: 1
Reflection冗長度: 4.05 % / : 420756 / Rmerge(I) obs: 0.112 / Χ2: 1 / D res high: 2.3 Å / D res low: 69.22 Å / Num. obs: 102988 / % possible obs: 97.8
Diffraction reflection shell

ID: 1

最高解像度 (Å)最低解像度 (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
4.9569.2298.60.0841.474.292202
3.934.9599.70.0941.134.27209
3.443.9398.80.1291.463.88562
3.123.4498.20.131.063.9562
2.93.1297.60.1560.953.9910
2.732.997.40.1860.864.016
2.592.7397.10.2680.973.9297
2.482.5997.20.2710.724.07
2.382.4896.60.3190.664.083
2.32.3896.50.3630.644.095
反射解像度: 2.3→69.22 Å / Num. all: 102988 / Num. obs: 102988 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 4.05 % / Biso Wilson estimate: 48.43 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Χ2: 1 / Net I/σ(I): 7.6 / Scaling rejects: 3156
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.3-2.384.090.3632.841457101350.6496.5
2.38-2.484.080.3193.241427101520.6696.6
2.48-2.594.070.2713.741434101870.7297.2
2.59-2.733.920.2684.139971101780.9797.1
2.73-2.94.010.1865.441111102390.8697.4
2.9-3.123.990.1566.641043102780.9597.6
3.12-3.443.950.138.340817103291.0698.2
3.44-3.933.880.1299.940969104231.4698.8
3.93-4.954.270.09413.245201105421.1399.7
4.95-69.224.290.08417.147326105251.4798.6

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
d*TREKデータスケーリング
d*TREK9.7 W8RSSIデータ削減
PHASER位相決定
PHENIX精密化
PDB_EXTRACT3.11データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 3QJ7
解像度: 2.3→45.0089 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7946 / Isotropic thermal model: isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: mlhl
Rfactor反射数%反射Selection details
Rfree0.2577 5139 4.99 %random
Rwork0.2126 ---
all0.2149 102895 --
obs0.2149 102895 97.7 %-
溶媒の処理Bsol: 49.64 Å2 / ksol: 0.347 e/Å3
原子変位パラメータBiso max: 178.13 Å2 / Biso mean: 57.2676 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-5.237 Å20 Å22.115 Å2
2---0.832 Å2-0 Å2
3----4.405 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→45.0089 Å
タンパク質核酸リガンド溶媒全体
原子数16473 0 416 352 17241
拘束条件
Refine-IDタイプDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.7671
X-RAY DIFFRACTIONf_bond_d0.0061
X-RAY DIFFRACTIONf_chiral_restr0.0561
X-RAY DIFFRACTIONf_dihedral_angle_d11.291
X-RAY DIFFRACTIONf_plane_restr0.0041
X-RAY DIFFRACTIONf_nbd_refined4.081
LS精密化 シェル
解像度 (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.3-2.30390.2782503X-RAY DIFFRACTION19691
2.3039-2.30790.2724459X-RAY DIFFRACTION19690
2.3079-2.31190.2863477X-RAY DIFFRACTION19691
2.3119-2.31590.2681512X-RAY DIFFRACTION19691
2.3159-2.31990.2509471X-RAY DIFFRACTION19692
2.3199-2.3240.2453522X-RAY DIFFRACTION19692
2.324-2.32810.2469478X-RAY DIFFRACTION19691
2.3281-2.33220.2626501X-RAY DIFFRACTION19692
2.3322-2.33630.2561518X-RAY DIFFRACTION19694
2.3363-2.34050.2539491X-RAY DIFFRACTION19692
2.3405-2.34470.2546476X-RAY DIFFRACTION19690
2.3447-2.3490.2433482X-RAY DIFFRACTION19693
2.349-2.35320.2565463X-RAY DIFFRACTION19694
2.3532-2.35750.2567526X-RAY DIFFRACTION19691
2.3575-2.36190.2491501X-RAY DIFFRACTION19694
2.3619-2.36620.2362484X-RAY DIFFRACTION19691
2.3662-2.37060.2642499X-RAY DIFFRACTION19692
2.3706-2.3750.2559524X-RAY DIFFRACTION19694
2.375-2.37950.2411476X-RAY DIFFRACTION19691
2.3795-2.3840.2515479X-RAY DIFFRACTION19692
2.384-2.38850.2452482X-RAY DIFFRACTION19690
2.3885-2.39310.2471511X-RAY DIFFRACTION19692
2.3931-2.39770.2505466X-RAY DIFFRACTION19690
2.3977-2.40230.2547504X-RAY DIFFRACTION19692
2.4023-2.4070.2551495X-RAY DIFFRACTION19692
2.407-2.41170.2648502X-RAY DIFFRACTION19692
2.4117-2.41650.27451X-RAY DIFFRACTION19692
2.4165-2.42130.2652471X-RAY DIFFRACTION19689
2.4213-2.42610.249535X-RAY DIFFRACTION19692
2.4261-2.43090.2662486X-RAY DIFFRACTION19691
2.4309-2.43580.2494516X-RAY DIFFRACTION19692
2.4358-2.44080.2551472X-RAY DIFFRACTION19693
2.4408-2.44580.2585466X-RAY DIFFRACTION19690
2.4458-2.45080.2592498X-RAY DIFFRACTION19693
2.4508-2.45590.2506479X-RAY DIFFRACTION19690
2.4559-2.4610.2612496X-RAY DIFFRACTION19693
2.461-2.46610.2629489X-RAY DIFFRACTION19692
2.4661-2.47130.2392529X-RAY DIFFRACTION19692
2.4713-2.47650.2393507X-RAY DIFFRACTION19692
2.4765-2.48180.241468X-RAY DIFFRACTION19692
2.4818-2.48710.2595477X-RAY DIFFRACTION19694
2.4871-2.49250.256504X-RAY DIFFRACTION19692
2.4925-2.49790.2322480X-RAY DIFFRACTION19691
2.4979-2.50340.2584497X-RAY DIFFRACTION19692
2.5034-2.50890.2304489X-RAY DIFFRACTION19693
2.5089-2.51450.2409530X-RAY DIFFRACTION19694
2.5145-2.52010.2584488X-RAY DIFFRACTION19692
2.5201-2.52570.2422490X-RAY DIFFRACTION19692
2.5257-2.53140.2402505X-RAY DIFFRACTION19694
2.5314-2.53720.2249495X-RAY DIFFRACTION19692
2.5372-2.5430.2479485X-RAY DIFFRACTION19693
2.543-2.54890.2401504X-RAY DIFFRACTION19692
2.5489-2.55480.2277512X-RAY DIFFRACTION19694
2.5548-2.56080.238520X-RAY DIFFRACTION19693
2.5608-2.56690.2484431X-RAY DIFFRACTION19691
2.5669-2.57290.2396482X-RAY DIFFRACTION19692
2.5729-2.57910.2358528X-RAY DIFFRACTION19692
2.5791-2.58530.2453498X-RAY DIFFRACTION19692
2.5853-2.59160.2542494X-RAY DIFFRACTION19692
2.5916-2.59790.2611478X-RAY DIFFRACTION19694
2.5979-2.60430.2367500X-RAY DIFFRACTION19689
2.6043-2.61080.2444503X-RAY DIFFRACTION19693
2.6108-2.61730.2476498X-RAY DIFFRACTION19692
2.6173-2.62390.2487484X-RAY DIFFRACTION19693
2.6239-2.63060.2612497X-RAY DIFFRACTION19693
2.6306-2.63730.2643480X-RAY DIFFRACTION19694
2.6373-2.64410.2665502X-RAY DIFFRACTION19693
2.6441-2.65090.2561515X-RAY DIFFRACTION19692
2.6509-2.65790.2672473X-RAY DIFFRACTION19691
2.6579-2.66490.2632513X-RAY DIFFRACTION19694
2.6649-2.6720.2734503X-RAY DIFFRACTION19693
2.672-2.67910.2721487X-RAY DIFFRACTION19691
2.6791-2.68640.2963486X-RAY DIFFRACTION19691
2.6864-2.69370.2704486X-RAY DIFFRACTION19691
2.6937-2.70110.2594530X-RAY DIFFRACTION19695
2.7011-2.70860.248497X-RAY DIFFRACTION19693
2.7086-2.71610.2555474X-RAY DIFFRACTION19692
2.7161-2.72380.2464469X-RAY DIFFRACTION19689
2.7238-2.73150.2524497X-RAY DIFFRACTION19692
2.7315-2.73940.254456X-RAY DIFFRACTION19691
2.7394-2.74730.2672523X-RAY DIFFRACTION19693
2.7473-2.75530.2456518X-RAY DIFFRACTION19693
2.7553-2.76340.2453505X-RAY DIFFRACTION19692
2.7634-2.77160.2588511X-RAY DIFFRACTION19691
2.7716-2.77990.2694476X-RAY DIFFRACTION19694
2.7799-2.78830.2365469X-RAY DIFFRACTION19693
2.7883-2.79680.2542532X-RAY DIFFRACTION19694
2.7968-2.80540.2431479X-RAY DIFFRACTION19693
2.8054-2.81410.2521459X-RAY DIFFRACTION19691
2.8141-2.82290.2411508X-RAY DIFFRACTION19693
2.8229-2.83180.2465522X-RAY DIFFRACTION19694
2.8318-2.84090.2306509X-RAY DIFFRACTION19692
2.8409-2.850.2546524X-RAY DIFFRACTION19693
2.85-2.85930.252470X-RAY DIFFRACTION19694
2.8593-2.86870.2333500X-RAY DIFFRACTION19693
2.8687-2.87830.253478X-RAY DIFFRACTION19694
2.8783-2.88790.2331499X-RAY DIFFRACTION19692
2.8879-2.89770.2298492X-RAY DIFFRACTION19692
2.8977-2.90760.2422510X-RAY DIFFRACTION19692
2.9076-2.91770.236500X-RAY DIFFRACTION19694
2.9177-2.92790.2551479X-RAY DIFFRACTION19690
2.9279-2.93820.2301524X-RAY DIFFRACTION19694
2.9382-2.94870.2452483X-RAY DIFFRACTION19692
2.9487-2.95940.2425508X-RAY DIFFRACTION19693
2.9594-2.97020.2292487X-RAY DIFFRACTION19695
2.9702-2.98110.2392464X-RAY DIFFRACTION19692
2.9811-2.99220.2342514X-RAY DIFFRACTION19692
2.9922-3.00350.221513X-RAY DIFFRACTION19693
3.0035-3.0150.2235494X-RAY DIFFRACTION19692
3.015-3.02660.2335476X-RAY DIFFRACTION19693
3.0266-3.03840.2254535X-RAY DIFFRACTION19695
3.0384-3.05040.2449474X-RAY DIFFRACTION19693
3.0504-3.06260.2662507X-RAY DIFFRACTION19695
3.0626-3.0750.2463523X-RAY DIFFRACTION19692
3.075-3.08760.2482479X-RAY DIFFRACTION19694
3.0876-3.10040.2454514X-RAY DIFFRACTION19695
3.1004-3.11350.2429476X-RAY DIFFRACTION19692
3.1135-3.12670.2524519X-RAY DIFFRACTION19692
3.1267-3.14020.2481516X-RAY DIFFRACTION19695
3.1402-3.15390.2313495X-RAY DIFFRACTION19693
3.1539-3.16780.217499X-RAY DIFFRACTION19694
3.1678-3.1820.2168481X-RAY DIFFRACTION19691
3.182-3.19650.2285490X-RAY DIFFRACTION19693
3.1965-3.21120.2072508X-RAY DIFFRACTION19693
3.2112-3.22620.2291500X-RAY DIFFRACTION19693
3.2262-3.24150.2174514X-RAY DIFFRACTION19693
3.2415-3.25710.2283512X-RAY DIFFRACTION19693
3.2571-3.2730.2092493X-RAY DIFFRACTION19694
3.273-3.28920.21493X-RAY DIFFRACTION19694
3.2892-3.30570.2047499X-RAY DIFFRACTION19695
3.3057-3.32250.189510X-RAY DIFFRACTION19693
3.3225-3.33980.2105524X-RAY DIFFRACTION19694
3.3398-3.35730.2153488X-RAY DIFFRACTION19694
3.3573-3.37530.2054520X-RAY DIFFRACTION19694
3.3753-3.39360.2004483X-RAY DIFFRACTION19694
3.3936-3.41240.2035515X-RAY DIFFRACTION19693
3.4124-3.43150.1981485X-RAY DIFFRACTION19693
3.4315-3.45110.2028535X-RAY DIFFRACTION19694
3.4511-3.47120.2213486X-RAY DIFFRACTION19693
3.4712-3.49170.2003484X-RAY DIFFRACTION19694
3.4917-3.51270.2143532X-RAY DIFFRACTION19693
3.5127-3.53430.2028483X-RAY DIFFRACTION19693
3.5343-3.55630.185530X-RAY DIFFRACTION19694
3.5563-3.5790.2038483X-RAY DIFFRACTION19693
3.579-3.60220.1929486X-RAY DIFFRACTION19693
3.6022-3.62610.1932505X-RAY DIFFRACTION19695
3.6261-3.65050.1978529X-RAY DIFFRACTION19694
3.6505-3.67570.1831499X-RAY DIFFRACTION19692
3.6757-3.70160.1947476X-RAY DIFFRACTION19692
3.7016-3.72820.1946516X-RAY DIFFRACTION19696
3.7282-3.75560.1926518X-RAY DIFFRACTION19694
3.7556-3.78380.1873500X-RAY DIFFRACTION19695
3.7838-3.81290.188519X-RAY DIFFRACTION19694
3.8129-3.84290.196522X-RAY DIFFRACTION19695
3.8429-3.87390.1986480X-RAY DIFFRACTION19691
3.8739-3.90590.1907474X-RAY DIFFRACTION19694
3.9059-3.9390.1992541X-RAY DIFFRACTION19694
3.939-3.97320.188509X-RAY DIFFRACTION19694
3.9732-4.00860.1838485X-RAY DIFFRACTION19695
4.0086-4.04540.1802536X-RAY DIFFRACTION19695
4.0454-4.08350.1682488X-RAY DIFFRACTION19694
4.0835-4.12320.1557511X-RAY DIFFRACTION19696
4.1232-4.16440.1645535X-RAY DIFFRACTION19693
4.1644-4.20730.1519488X-RAY DIFFRACTION19695
4.2073-4.2520.1478496X-RAY DIFFRACTION19693
4.252-4.29870.1354511X-RAY DIFFRACTION19694
4.2987-4.34750.1422530X-RAY DIFFRACTION19694
4.3475-4.39860.1253498X-RAY DIFFRACTION19694
4.3986-4.45220.125488X-RAY DIFFRACTION19695
4.4522-4.50850.1414534X-RAY DIFFRACTION19695
4.5085-4.56780.136505X-RAY DIFFRACTION19695
4.5678-4.63030.1458504X-RAY DIFFRACTION19693
4.6303-4.69630.1502490X-RAY DIFFRACTION19694
4.6963-4.76640.1279537X-RAY DIFFRACTION19694
4.7664-4.84080.1488478X-RAY DIFFRACTION19693
4.8408-4.920.14509X-RAY DIFFRACTION19694
4.92-5.00480.1508523X-RAY DIFFRACTION19695
5.0048-5.09570.154509X-RAY DIFFRACTION19695
5.0957-5.19350.1439526X-RAY DIFFRACTION19695
5.1935-5.29940.1614516X-RAY DIFFRACTION19695
5.2994-5.41440.1471512X-RAY DIFFRACTION19694
5.4144-5.54010.1639509X-RAY DIFFRACTION19695
5.5401-5.67840.1652519X-RAY DIFFRACTION19696
5.6784-5.83170.1707501X-RAY DIFFRACTION19695
5.8317-6.00290.1644519X-RAY DIFFRACTION19695
6.0029-6.19620.1805514X-RAY DIFFRACTION19696
6.1962-6.4170.189509X-RAY DIFFRACTION19693
6.417-6.67320.1752533X-RAY DIFFRACTION19695
6.6732-6.97580.1791501X-RAY DIFFRACTION19695
6.9758-7.34210.1628515X-RAY DIFFRACTION19694
7.3421-7.79990.1611519X-RAY DIFFRACTION19695
7.7999-8.39850.1738507X-RAY DIFFRACTION19694
8.3985-9.23710.1759511X-RAY DIFFRACTION19693
9.2371-10.55870.1763490X-RAY DIFFRACTION19689
10.5587-13.24640.1779491X-RAY DIFFRACTION19689
13.2464-45.01750.3011422X-RAY DIFFRACTION19675
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.51740.62580.1121.310.50941.25060.1164-0.10820.09440.2603-0.14060.25760.0224-0.19990.02050.3308-0.07720.00380.2357-0.00770.3007-22.8484-14.338648.5831
20.8752-0.36260.79371.21740.84790.18140.1660.12270.1787-0.5195-0.09490.1439-0.43740.0995-0.02030.4074-0.00970.00870.20950.0470.2567-18.5491-3.619235.3796
30.3662-0.1672-0.02182.03741.25940.82520.07420.0302-0.0850.2112-0.20810.1992-0.1355-0.16210.12810.319-0.0811-0.02440.22620.0210.2251-18.2785-14.796848.5313
41.0058-0.1232-0.71341.34931.94550.74070.08640.0706-0.20220.4997-0.24450.18290.2161-0.22650.150.3493-0.0879-0.00840.2148-0.04190.2687-21.1193-26.120237.3341
51.3635-1.1484-0.56540.94010.98610.3612-0.18970.55680.1383-0.0938-0.0649-0.65480.0969-0.38890.14780.4853-0.16180.06360.36840.00470.5128-32.4898-20.849556.6506
61.18570.86650.06522.36460.840.3967-0.18340.3167-0.0122-0.49720.444-0.2436-0.35720.3645-0.1640.3516-0.10410.0140.2923-0.06190.30165.8013-8.708945.0651
70.64280.45690.2861.38690.6350.83710.14860.04130.267-0.29250.1019-0.1642-0.46250.0921-0.21530.4104-0.11590.12820.2086-0.04640.2643-4.59618.5846.6739
86.08682.90675.89895.92623.50262.657-0.53270.11431.3147-0.0036-0.46911.6010.0457-0.56510.76250.1769-0.06930.11630.5251-0.24290.389518.5509-5.858845.3082
9-0.0996-0.6169-0.46420.94791.25620.9226-0.1872-0.46980.48010.07290.6553-0.504-0.2080.3252-0.35320.4095-0.22230.1220.4387-0.26630.48355.161912.353358.536
106.7295-0.87561.1553-0.29894.99431.93571.2246-0.2031.97660.1330.2402-0.03620.9087-0.5418-0.93650.5115-0.0845-0.02010.3761-0.08570.549818.67414.261646.7992
112.43830.18550.62682.24991.67315.66830.120.42290.2039-0.60020.28160.1401-0.46691.4349-0.29080.32290.10560.05220.60370.0390.3085-14.7785-22.6525-4.0209
120.6394-1.1787-0.20251.3216-1.5084-0.64190.21690.39370.0049-0.7051-0.5325-0.371-0.14170.64650.27140.51650.15660.08220.580.05580.2885-9.9193-29.1586-7.818
132.3080.0918-0.21870.23861.10750.9492-0.1039-0.0829-0.2867-0.4676-0.3232-0.3106-0.31871.50180.40520.53620.27910.26941.34440.37990.522310.7462-34.7901-7.5337
140.96740.1325-1.93691.471-0.50852.82240.06310.2332-0.0195-0.6921-0.5936-0.37550.35170.93640.24390.43790.32750.10070.59090.08840.2189-3.4131-38.0559-8.7443
155.1446-0.9318-3.42251.7149-1.7466-3.6746-0.04571.3109-0.5741-0.9736-0.539-0.26610.7256-0.43020.37230.52120.03310.21870.73460.33360.2365-4.434-18.166-17.6791
161.8419-0.521-1.0890.5977-0.69241.1054-0.14460.0161-0.3284-0.04520.13040.30870.660.46250.0660.49190.1949-0.08160.4188-0.0960.3922-20.7122-49.6733.9742
17-0.236-0.0192-1.31711.6189-1.2122.0939-0.0994-0.0011-0.29220.0201-0.2676-0.02810.09280.21030.33330.1380.0079-0.0120.23890.04220.2832-13.2238-44.295923.7105
180.0161-0.55350.47681.9118-1.08163.05090.1005-0.0372-0.0331-0.1091-0.5985-0.4834-0.00631.2880.49050.11210.07840.02110.53520.20960.3518-0.2366-38.952215.4352
19-0.0219-1.1366-0.63870.8236-0.52262.1866-0.06550.2167-0.1624-0.0351-0.10160.01270.18780.30590.14860.19140.0593-0.01580.2763-0.01310.2821-15.0263-41.506613.3704
200.48442.16030.23872.44440.48181.98660.01040.171-0.20980.2617-0.1574-0.03620.18680.02630.15590.1330.02280.00460.1563-0.09390.2913-21.3142-40.873724.1303
211.94290.61020.06711.4736-0.06891.66950.0007-0.23-0.16420.7615-0.150.20370.6925-0.08550.13830.6526-0.09440.02210.2545-0.03790.2582-50.5165-14.1371.5482
221.5262-0.8476-1.3740.2343-2.05212.6819-0.3895-0.4691-1.68570.544-0.926-0.35460.03090.33991.13720.4456-0.33620.23720.8419-0.10631.0386-66.8371-4.01640.6689
230.61-0.3644-0.1341.913-1.44713.4158-0.2681-0.0224-0.3941-0.161-0.6152-0.19310.35370.29160.57780.2567-0.0187-0.08890.27280.00310.3407-55.86621.9919-10.5196
241.3772-0.65670.86193.17551.1097-0.34850.15270.1835-0.11060.2621-0.15570.2310.442-0.01650.01330.43480.0046-0.04420.26680.02880.1899-44.9094-7.6961-6.0066
251.46410.56680.25491.32881.4772.89460.18650.1669-0.36270.5901-0.32830.27571.3048-0.0120.11580.9695-0.0821-0.01540.1903-0.04570.3042-50.6151-24.1054-5.3465
261.4969-1.49451.21191.7718-1.14528.3958-1.0368-0.0255-0.17040.263-0.6224-0.19550.20561.36990.88610.43440.13550.0240.64580.17130.4809-19.4521-7.07280.0902
271.449-1.0357-0.19481.8236-0.54621.52680.03140.21060.5120.2251-0.2806-0.66780.12040.6270.26030.294-0.1113-0.15960.43040.13970.4596-25.66158.8364-2.0537
280.88790.3418-0.0673.133-1.30422.0805-0.24770.13390.3037-0.06850.0594-0.7581-0.0625-0.24970.14850.309-0.0221-0.00530.31530.15460.4641-36.894516.6117-8.961
290.2358-0.27540.98173.33350.04340.9333-0.01360.04550.20270.5937-0.1113-0.25650.04830.11380.1220.3714-0.0112-0.07980.31080.05470.2452-37.41916.54833.0843
30-0.11590.83660.10221.6361-0.09331.8479-0.23930.0130.48860.34590.1388-0.82950.12350.95650.16370.4005-0.0413-0.27840.720.05340.6926-19.20729.05815.0684
311.43060.6636-2.56042.1472-1.083.1964-0.0012-0.3358-0.314-0.0979-0.3105-0.4964-0.22990.78830.31450.1207-0.0146-0.00350.45540.00790.347728.8237-26.562438.0201
32-0.0417-0.2744-3.04351.3714-0.36514.3922-0.1844-1.2233-0.3926-0.1766-0.7674-0.72270.42521.73360.89050.07780.21430.080.83180.47610.912939.4291-41.380342.7719
33-0.9392-0.3293-2.26791.5624-1.79134.8361-0.356-1.1142-0.74080.6061-0.8324-0.46960.24281.71131.34850.14940.0530.02150.84820.23950.695434.1335-37.316246.7232
341.39310.3582-2.39680.8716-0.68372.1866-0.3285-0.0749-0.4714-0.0255-0.0574-0.59580.14190.50880.3650.23860.00060.04310.36480.02740.476327.2066-33.099938.5349
351.70990.7663-1.69822.45690.04172.66220.00140.3285-0.3375-0.712-0.4222-0.3141-0.28120.0660.31810.33260.07860.09510.4824-0.01730.435529.8369-29.293426.4629
362.62211.542-0.9830.94731.1074.8322-0.39050.1721-0.48620.311-0.1342-0.16940.8704-0.65050.45630.35840.00950.06210.4628-0.07510.4969.8872-43.799148.4563
37-1.1867-0.4036-1.11710.9312-0.42374.8895-0.1419-0.4898-0.22960.3063-0.4899-0.25550.11991.25560.5670.2437-0.0382-0.12770.75740.30270.550925.0266-41.727466.4161
38-2.1452-1.8312-1.133-0.4989-0.3762.23-0.1084-0.18130.84590.0009-0.1961-0.65270.86011.30370.54030.20260.240.06250.65360.41520.887830.586-45.691956.5386
391.28390.8088-2.53320.2912-1.56563.9412-0.0448-0.4257-0.65110.3475-0.529-0.4766-0.07940.37620.51930.2517-0.0671-0.09140.40560.0560.435217.7062-36.87758.5652
401.014-0.3897-2.22021.6694-1.25383.567-0.2009-0.2656-0.19850.5046-0.48840.2015-0.46740.07190.58580.3502-0.0906-0.05480.5356-0.01460.36879.8184-36.592269.7009
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:80)A1 - 80
2X-RAY DIFFRACTION2(chain A and resid 81:158)A81 - 158
3X-RAY DIFFRACTION3(chain A and resid 159:222)A159 - 222
4X-RAY DIFFRACTION4(chain A and resid 223:254)A223 - 254
5X-RAY DIFFRACTION5(chain A and resid 255:261)A255 - 261
6X-RAY DIFFRACTION6(chain B and resid 1:35)B1 - 35
7X-RAY DIFFRACTION7(chain B and resid 36:212)B36 - 212
8X-RAY DIFFRACTION8(chain B and resid 213:217)B213 - 217
9X-RAY DIFFRACTION9(chain B and resid 218:253)B218 - 253
10X-RAY DIFFRACTION10(chain B and resid 254:261)B254 - 261
11X-RAY DIFFRACTION11(chain C and resid 1:20)C1 - 20
12X-RAY DIFFRACTION12(chain C and resid 21:49)C21 - 49
13X-RAY DIFFRACTION13(chain C and resid 50:109)C50 - 109
14X-RAY DIFFRACTION14(chain C and resid 110:253)C110 - 253
15X-RAY DIFFRACTION15(chain C and resid 254:261)C254 - 261
16X-RAY DIFFRACTION16(chain D and resid 1:33)D1 - 33
17X-RAY DIFFRACTION17(chain D and resid 34:81)D34 - 81
18X-RAY DIFFRACTION18(chain D and resid 82:158)D82 - 158
19X-RAY DIFFRACTION19(chain D and resid 159:216)D159 - 216
20X-RAY DIFFRACTION20(chain D and resid 217:263)D217 - 263
21X-RAY DIFFRACTION21(chain E and resid 1:80)E1 - 80
22X-RAY DIFFRACTION22(chain E and resid 81:86)E81 - 86
23X-RAY DIFFRACTION23(chain E and resid 87:106)E87 - 106
24X-RAY DIFFRACTION24(chain E and resid 107:216)E107 - 216
25X-RAY DIFFRACTION25(chain E and resid 217:260)E217 - 260
26X-RAY DIFFRACTION26(chain F and resid 1:14)F1 - 14
27X-RAY DIFFRACTION27(chain F and resid 15:80)F15 - 80
28X-RAY DIFFRACTION28(chain F and resid 81:104)F81 - 104
29X-RAY DIFFRACTION29(chain F and resid 105:207)F105 - 207
30X-RAY DIFFRACTION30(chain F and resid 208:261)F208 - 261
31X-RAY DIFFRACTION31(chain G and resid 1:69)G1 - 69
32X-RAY DIFFRACTION32(chain G and resid 70:137)G70 - 137
33X-RAY DIFFRACTION33(chain G and resid 138:154)G138 - 154
34X-RAY DIFFRACTION34(chain G and resid 155:213)G155 - 213
35X-RAY DIFFRACTION35(chain G and resid 214:260)G214 - 260
36X-RAY DIFFRACTION36(chain H and resid 1:35)H1 - 35
37X-RAY DIFFRACTION37(chain H and resid 36:127)H36 - 127
38X-RAY DIFFRACTION38(chain H and resid 128:149)H128 - 149
39X-RAY DIFFRACTION39(chain H and resid 150:216)H150 - 216
40X-RAY DIFFRACTION40(chain H and resid 217:259)H217 - 259

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万見について

-
お知らせ

-
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

+
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

+
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