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- PDB-8qn5: M. tuberculosis salicylate synthase MbtI in complex with methyl-A... -

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基本情報

登録情報
データベース: PDB / ID: 8qn5
タイトルM. tuberculosis salicylate synthase MbtI in complex with methyl-AMT (new crystal form)
要素Salicylate synthase
キーワードLYASE / salicylate / isochorismate / chorismate / mycobactins
機能・相同性
機能・相同性情報


isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity ...isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity / response to host immune response / tryptophan biosynthetic process / magnesium ion binding / plasma membrane
類似検索 - 分子機能
Salicylate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme
類似検索 - ドメイン・相同性
Chem-0GA / CITRATE ANION / AMMONIUM ION / Salicylate synthase
類似検索 - 構成要素
生物種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: 1.544 Å
データ登録者Mori, M. / Villa, S. / Meneghetti, M. / Bellinzoni, M.
資金援助 イタリア, 1件
組織認可番号国
University and Research - University of Milan イタリア
引用ジャーナル: Pharmaceuticals / 年: 2023
タイトル: Structural Study of a New MbtI-Inhibitor Complex: Towards an Optimized Model for Structure-Based Drug Discovery.
著者: Mori, M. / Villa, S. / Chiarelli, L.R. / Meneghetti, F. / Bellinzoni, M.
履歴
登録2023年9月25日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年11月15日Provider: repository / タイプ: Initial release
改定 1.12023年12月6日Group: Database references / Other / カテゴリ: citation / pdbx_database_status
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_database_status.status_code_sf

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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: Salicylate synthase
B: Salicylate synthase
C: Salicylate synthase
D: Salicylate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)197,64318
ポリマ－195,7984
非ポリマー1,84614
水25,5451418
1
A: Salicylate synthase
ヘテロ分子


  • 登録者が定義した集合体
  • 根拠: gel filtration
  • 49.6 kDa, 1 ポリマー
分子量 (理論値)分子数
合計 (水以外)49,5615
ポリマ－48,9491
非ポリマー6114
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Salicylate synthase
ヘテロ分子


  • 登録者が定義した集合体
  • 49.3 kDa, 1 ポリマー
分子量 (理論値)分子数
合計 (水以外)49,2984
ポリマ－48,9491
非ポリマー3483
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Salicylate synthase
ヘテロ分子


  • 登録者が定義した集合体
  • 49.3 kDa, 1 ポリマー
分子量 (理論値)分子数
合計 (水以外)49,3165
ポリマ－48,9491
非ポリマー3664
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Salicylate synthase
ヘテロ分子


  • 登録者が定義した集合体
  • 49.5 kDa, 1 ポリマー
分子量 (理論値)分子数
合計 (水以外)49,4694
ポリマ－48,9491
非ポリマー5193
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)95.635, 83.064, 126.258
Angle α, β, γ (deg.)90, 111.66, 90
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Salicylate synthase


分子量: 48949.383 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Mycobacterium tuberculosis H37Rv (結核菌)
遺伝子: mbtI / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P9WFX1

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非ポリマー , 5種, 1432分子

#2: 化合物
ChemComp-0GA / 3-{[(1Z)-1-carboxyprop-1-en-1-yl]oxy}-2-hydroxybenzoic acid


分子量: 238.193 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C11H10O6 / タイプ: SUBJECT OF INVESTIGATION
#3: 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: 5 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物 ChemComp-FLC / CITRATE ANION / シトラ-ト


分子量: 189.100 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H5O7
#5: 化合物 ChemComp-NH4 / AMMONIUM ION / アンモニウム


分子量: 18.038 Da / 分子数: 3 / 由来タイプ: 合成 / 式: H4N
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1418 / 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: 2.51 Å3/Da / 溶媒含有率: 50.99 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.6
詳細: 16% PEG 3350, 0.1 M sodium citrate pH 5.6, 2% tacsimate

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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: 0.980131 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2019年4月15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: 0.980131 Å / 相対比: 1
反射解像度: 1.544→117.345 Å / Num. obs: 211264 / % possible obs: 94.7 % / 冗長度: 7.04 %
詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.998 / CC1/2 anomalous: -0.166 / Rmerge(I) obs: 0.0672 / Rpim(I) all: 0.0272 / Rrim(I) all: 0.0726 / AbsDiff over sigma anomalous: 0.598 / Baniso tensor eigenvalue 1: 0 Å2 / Baniso tensor eigenvalue 2: 5.321 Å2 / Baniso tensor eigenvalue 3: 4.4751 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9984 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.0563 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.0563 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9984 / Aniso diffraction limit 1: 1.544 Å / Aniso diffraction limit 2: 1.697 Å / Aniso diffraction limit 3: 1.702 Å / Aniso diffraction limit axis 1 ortho1: 0.99027 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.13941 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.13941 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.99027 / Net I/σ(I): 12.57 / Num. measured all: 1487808 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.6 / % possible ellipsoidal: 94.7 / % possible ellipsoidal anomalous: 94.6 / % possible spherical: 78.6 / % possible spherical anomalous: 78.2 / Redundancy anomalous: 3.58 / Signal type: local
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
4.583-117.3457.070.036136.07747147471410563105630.997-0.0810.01490.03910.52199.810099.810099.83.7100
3.627-4.5837.110.040534.78750667506610563105630.998-0.2870.01640.04370.6031001001001001003.64100
3.163-3.6276.770.048729.69715137151310564105640.997-0.2830.02010.05270.63799.799.899.799.899.73.4699.8
2.871-3.1637.020.058925.08741917419110563105630.997-0.2180.02390.06360.63310099.810099.81003.5799.8
2.663-2.8717.230.069820.87763607636010563105630.995-0.1970.02790.07530.63199.999.699.999.699.93.6799.6
2.505-2.6637.320.08217.9773517735110563105630.994-0.1440.03250.08830.64699.799.599.799.599.73.7299.5
2.378-2.5057.380.09515.44779507795010563105630.993-0.0990.03740.10220.63199.699.499.699.499.63.7499.4
2.273-2.3787.090.109113.28749447494410564105640.992-0.080.04390.11770.64599.599.399.599.399.53.5999.3
2.185-2.2736.750.133911.14713227132210563105630.989-0.070.05530.1450.66199.499.199.499.199.43.4299.1
2.109-2.1857.130.16719.61753557535510563105630.986-0.0450.06690.18020.68899.399.199.399.199.33.6199.1
2.042-2.1097.220.19548.07762187621810563105630.9830.0130.07770.21040.67599.298.999.298.999.23.6598.9
1.983-2.0427.290.23026.7770077700710563105630.9780.040.09110.24780.64699.198.899.198.899.13.6898.8
1.93-1.9836.760.27455.1714497144910564105640.9630.0780.11330.29730.61498.998.798.998.798.93.4298.7
1.882-1.936.780.33794.05715787157810563105630.9470.0820.140.36620.58798.998.698.998.698.93.4298.6
1.839-1.8827.050.41913.31744897448910563105630.9260.0040.1690.45230.5598.798.598.798.598.73.5698.5
1.799-1.8397.130.50152.74753237532310563105630.9080.0120.20070.54060.53398.698.498.698.498.63.698.4
1.763-1.7997.210.61222.27761417614110563105630.870.0120.24320.65930.52298.498.198.498.198.43.6498.1
1.728-1.7637.240.73491.88764737647310564105640.8310.0010.29170.79130.51396.596.296.596.296.53.6596.2
1.684-1.7287.120.80081.74751767517610563105630.7850.0120.32030.86330.51874.374.174.368.568.73.5974.1
1.544-1.6846.170.79821.62651886518810563105630.752-0.010.33860.86950.50457.662.157.617.215.83.3162.1

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解析

ソフトウェア
名称バージョン分類
BUSTER2.10.4精密化
autoPROC1.0.5 20230726data processing
autoPROCJun 30, 2023data processing
Aimless0.7.13データスケーリング
autoPROC2.3.94data processing
autoPROCデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.544→117.34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.094 / 交差検証法: THROUGHOUT / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.091
Rfactor反射数%反射Selection details
Rfree0.2078 10546 -RANDOM
Rwork0.1828 ---
obs0.184 211264 78.6 %-
原子変位パラメータBiso mean: 33.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.4405 Å20 Å2-0.079 Å2
2--0.7168 Å20 Å2
3----0.2763 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
精密化ステップサイクル: LAST / 解像度: 1.544→117.34 Å
タンパク質核酸リガンド溶媒全体
原子数12855 0 127 1418 14400
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113340HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9718164HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6217SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2363HARMONIC5
X-RAY DIFFRACTIONt_it13340HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1761SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact13593SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion2.42
LS精密化 シェル解像度: 1.544→1.64 Å
Rfactor反射数%反射
Rfree0.2994 218 -
Rwork0.259 --
obs--9.61 %
精密化 TLS

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1185-0.1690.70481.7891-0.29621.62160.03470.1862-0.25560.1862-0.1015-0.0001-0.2556-0.00010.06680.0352-0.01540.00180.0421-0.06570.0706-22.4134-0.1093-0.3726
20.8416-0.0315-0.31953.80641.37141.97270.08450.11660.2780.1166-0.02410.03760.2780.0376-0.06040.01690.0215-0.03120.04060.02020.0454-21.8417-24.4504-3.8536
31.9403-0.68270.36351.68380.39744.19830.04410.02080.13850.0208-0.011-0.08190.1385-0.0819-0.03310.0835-0.01390.00360.05730.02430.0724-31.1735-27.4121-4.4482
40.80160.1855-0.60381.2330.57431.5745-0.03-0.00140.159-0.0014-0.0295-0.05780.159-0.05780.0595-0.01560.0084-0.0083-0.0263-0.0028-0.0397-33.2054-19.7272-11.4105
51.72140.80750.66311.70730.62942.15780.0740.1190.05270.119-0.08210.01020.05270.01020.0082-0.01430.0160.00090.03120.00150.016-26.4062-13.0487-3.9454
60.9436-0.55141.92121.99470.49291.377-0.0470.365-0.28630.365-0.35630.5529-0.28630.55290.40320.2538-0.0988-0.02640.248-0.04330.2724-14.49243.45972.3829
71.29390.09940.30650.62380.10611.0579-0.0488-0.1264-0.0999-0.1264-0.01140.0101-0.09990.01010.06020.0170.0141-0.01730.02520.01620.0403-29.406-6.0784-21.2165
812.61231.4814-10.586122.3307-40.051179.28070.80821.3107-2.5291.31070.2333-0.7558-2.529-0.7558-1.04150.030.04670.02060.21160.11750.2632-45.4895-4.55-15.9134
96.1565-2.70662.543311.9612-6.30536.47490.1048-0.2396-0.2552-0.2396-0.0290.1263-0.25520.1263-0.07570.13150.01740.05940.2534-0.03340.2693-51.1712-5.4179-22.4738
104.6806-4.81793.58645.451-2.52994.3137-0.12450.1146-0.0820.1146-0.0542-0.0741-0.082-0.07410.17870.0859-0.00420.00170.2739-0.00870.2414-49.5757-10.2446-9.7104
110.9890.04760.31190.68960.10381.6158-0.019-0.06020.0917-0.0602-0.0437-0.14180.0917-0.14180.0627-0.00770.0142-0.02440.0289-0.00150.0074-33.9605-13.2623-20.0238
125.27891.88313.65513.22242.01115.1429-0.1748-0.2601-0.2378-0.2601-0.02060.0085-0.23780.00850.19550.1389-0.0016-0.01270.0980.06740.1452-27.09140.3544-27.0451
130.5750.1826-0.5893.0167-1.37294.8009-0.0496-0.15510.2647-0.1551-0.057-0.08620.2647-0.08620.10660.0991-0.0208-0.01370.1016-0.01420.2111.5705-22.9089-9.1013
141.44270.6599-0.06322.30180.04960.75150.04210.0425-0.07340.0425-0.0545-0.0398-0.0734-0.03980.0124-0.01650.0092-0.0034-0.0011-0.0056-0.00433.56620.7873-8.8267
154.58320.606-2.720813.9639-6.93728.0888-0.07470.2566-0.15240.25660.1119-0.0719-0.1524-0.0719-0.03720.0842-0.0137-0.02390.0807-0.04620.06318.73743.9753-1.1675
161.48090.6466-0.37331.3117-0.80851.24680.0239-0.058-0.0069-0.058-0.01980.0131-0.00690.0131-0.0042-0.03810.0142-0.0042-0.0227-0.0055-0.03525.712-5.3574-9.9709
173.16223.0703-5.78885.242-6.790716.1374-0.1448-0.81780.2913-0.81780.3566-0.39210.2913-0.3921-0.21180.4023-0.0773-0.02420.3345-0.13090.24830.3349-21.1422-26.3698
180.72524.00326.632518.36862.215717.0951-1.1156-2.2620.9122-2.2620.7163-0.14760.9122-0.14760.39930.8523-0.08330.09550.43950.02050.042914.1467-1.5524-41.8733
191.762-0.0389-0.58471.5292-0.08140.94480.0138-0.35960.0649-0.35960.0069-0.07070.0649-0.0707-0.02070.12820.0250.03160.1232-0.00940.039514.1074-7.2339-23.6773
203.0347-0.1218-0.3324.36662.9193.5940.0231-0.26340.2496-0.26340.06050.05660.24960.0566-0.08350.18010.04270.0020.2407-0.05230.166132.3305-12.7166-26.7257
210.5796-1.423-1.31382.51441.76072.9415-0.03310.03030.08760.03030.10820.23620.08760.2362-0.07510.05630.0034-0.00610.1972-0.05990.166529.9056-6.7396-12.2525
221.40440.0768-0.05511.6916-0.30261.63090.0041-0.2830.0045-0.283-0.08220.00210.00450.00210.0780.04050.03880.0320.07910.02320.030815.8913-0.3393-22.1857
2311.94721.11395.47313.87518.848613.5631-0.7474-1.80890.7595-1.80890.43070.37930.75950.37930.31670.83690.00180.47660.5088-0.05490.411925.5115-4.2299-41.3574
247.43875.5274-2.1977.6926-1.43894.8119-0.0307-0.9790.0683-0.9790.0132-0.14770.0683-0.14770.01760.41870.03140.0340.2727-0.09870.134710.0124-13.8843-32.3611
250.47150.7018-0.46955.34434.75788.5979-0.12780.54850.73370.5485-0.15480.12640.73370.12640.28260.3110.0430.08380.16360.01760.282-26.0426-67.525-47.128
261.3682-0.9688-0.44622.55050.12021.13190.0996-0.0951-0.0194-0.0951-0.1562-0.0005-0.0194-0.00050.05660.0943-0.00230.01780.093-0.00910.1127-27.2046-44.1032-51.9021
273.3972-3.2218-1.665917.58814.22424.10140.1993-0.7416-0.1914-0.7416-0.2492-0.1147-0.1914-0.11470.04990.21120.04720.0020.2372-0.00640.1645-32.6907-42.9506-60.3495
281.0324-0.7387-0.88771.82641.28991.7347-0.05540.27490.20650.2749-0.02310.02620.20650.02620.07850.1324-0.04140.02190.1026-0.01390.1164-31.7678-48.384-38.5416
293.3156-0.089-1.20721.83990.37613.7615-0.15350.23770.34130.2377-0.1079-0.25730.3413-0.25730.26140.1445-0.03870.05190.0764-0.03840.1257-34.5335-52.9863-40.5397
3014.55766.535711.248413.87420.845669.010.12660.62612.58340.62610.89880.10182.58340.1018-1.02540.0584-0.0648-0.07010.3423-0.12110.1262-50.1591-51.1552-49.1579
3121.5081-4.17315.510413.3848-10.930413.58920.75750.78522.34020.7852-0.6644-0.20422.3402-0.2042-0.09310.6644-0.04610.10921.03750.28830.0466-56.4258-55.5265-27.1099
3214.0346.0983-5.8948.6784-3.385617.76030.48140.5067-0.15640.5067-0.50220.4809-0.15640.48090.02080.0015-0.06780.05190.2692-0.03760.4004-57.8141-46.4471-42.6522
3314.17566.4709-3.15629.3555-14.872182.105-0.052-0.26250.3094-0.2625-0.22871.610.30941.610.2807-0.2647-0.0289-0.03540.0367-0.0405-0.04-53.8499-50.5618-45.8062
341.03270.83231.01593.6732.37813.3903-0.0695-0.3149-0.3278-0.3149-0.074-0.1698-0.3278-0.16980.14350.149-0.03370.02270.1623-0.0660.1688-45.1333-37.0564-42.1682
351.6968-0.7625-2.03591.70771.00042.5094-0.00170.16830.1610.1683-0.1378-0.15340.161-0.15340.13950.0948-0.03940.03320.0528-0.02690.0793-35.552-45.4228-38.3397
365.7087-3.7393-3.02225.72982.44713.848-0.18450.80620.65230.8062-0.0746-0.05620.6523-0.05620.25910.436-0.0820.10570.20880.00710.195-39.6042-49.1026-23.4659
375.3132.11820.45022.38670.53692.0844-0.1826-0.3434-0.3908-0.34340.12740.2297-0.39080.22970.05520.1981-0.0556-0.02440.23660.0510.0967-1.6549-47.5342-61.2197
387.49741.13635.69641.10120.58179.8670.51360.19610.92430.1961-0.0078-00.9243-0-0.50590.2884-0.0272-0.06510.18630.01720.3493-0.0143-70.7092-48.1851
392.76656.0016.24751.46920.6234.53330.2954-0.48340.7117-0.48340.35850.650.71170.65-0.65380.29260.07110.01840.3087-0.09030.3327.6639-68.4939-55.3282
402.7477-0.81442.52841.1269-1.40955.45840.0072-0.0474-0.0358-0.0474-0.00370.2068-0.03580.2068-0.00340.1147-0.04950.00170.1872-0.01190.09383.6652-58.5856-51.48
41-0.9135.1064-3.01787.11219.650220.9889-0.5137-0.121-0.2651-0.121-0.1316-0.7203-0.2651-0.72030.64530.96970.3148-0.40070.4171-0.06490.3857-9.0309-42.8606-66.1324
421.9470.3440.86791.5125-0.27891.7781-0.06430.2936-0.32270.2936-0.0961-0.0477-0.3227-0.04770.16030.2333-0.05020.01450.2253-0.05080.14213.0078-44.5327-37.9658
4311.0047-2.8215-2.47566.5536.956713.699-0.1847-0.5894-0.51-0.58940.6373-0.1195-0.51-0.1195-0.45250.1047-0.06360.05560.3637-0.07240.258620.3762-53.2931-50.9582
4429.53298.9579-0.748844.436313.293728.1784-0.4334-0.40890.4921-0.4089-1.172-1.20950.4921-1.20951.60550.5918-0.30810.26140.3548-0.40930.735524.7928-32.9418-39.8784
458.41873.4645-0.306635.803212.137411.76150.43370.4682-0.62940.46820.01270.3669-0.62940.3669-0.44640.1943-0.07510.07920.2999-0.02840.343827.6038-49.6323-38.0281
467.70987.14391.370810.92082.67784.3764-0.0397-0.2889-0.0623-0.2889-0.0988-0.0233-0.0623-0.02330.13850.1344-0.00450.03990.2991-0.06470.316825.6201-53.0536-48.9808
472.02250.13020.5151.4826-0.03392.0355-0.02770.2785-0.09650.2785-0.10860.1274-0.09650.12740.13630.2041-0.0799-0.00770.2673-0.0110.13049.4671-50.5025-36.9619
4822.33132.56389.77719.305-0.24567.71620.0331-0.1728-0.1813-0.17280.0274-0.2608-0.1813-0.2608-0.06050.24350.0144-0.00430.1954-0.09510.2419-6.2132-38.6474-43.6938
497.261114.5767-13.38289.3791-2.451743.69990.14590.3329-0.570.3329-0.0047-1.6545-0.57-1.6545-0.1412-0.15520.0514-0.0098-0.09520.0132-0.0609-36.9868-4.3067-22.8803
507.02211.874213.87110-5.815125.2596-0.1892-0.03450.4869-0.03450.20470.88210.48690.8821-0.01550.050.09710.102-0.01880.0021-0.0520.7773-8.0716-27.3647
514.466516.26488.81125.457217.216919.9227-0.1769-0.28920.6906-0.2892-0.3561-2.83960.6906-2.83960.5330.1585-0.11460.05070.2118-0.03680.1663-44.3435-47.9658-31.8852
5210.2897-13.68823.37344.889713.946316.2017-0.2462-0.4414-0.7742-0.44140.62972.0353-0.77422.0353-0.38350.0956-0.1318-0.01870.2174-0.03860.075512.6664-43.9029-38.1024
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|16 - A|56 }A16 - 56
2X-RAY DIFFRACTION2{ A|57 - A|80 }A57 - 80
3X-RAY DIFFRACTION3{ A|81 - A|101 }A81 - 101
4X-RAY DIFFRACTION4{ A|102 - A|121 }A102 - 121
5X-RAY DIFFRACTION5{ A|122 - A|153 }A122 - 153
6X-RAY DIFFRACTION6{ A|154 - A|174 }A154 - 174
7X-RAY DIFFRACTION7{ A|175 - A|262 }A175 - 262
8X-RAY DIFFRACTION8{ A|263 - A|272 }A263 - 272
9X-RAY DIFFRACTION9{ A|273 - A|309 }A273 - 309
10X-RAY DIFFRACTION10{ A|310 - A|350 }A310 - 350
11X-RAY DIFFRACTION11{ A|351 - A|426 }A351 - 426
12X-RAY DIFFRACTION12{ A|427 - A|450 }A427 - 450
13X-RAY DIFFRACTION13{ B|15 - B|39 }B15 - 39
14X-RAY DIFFRACTION14{ B|40 - B|89 }B40 - 89
15X-RAY DIFFRACTION15{ B|90 - B|103 }B90 - 103
16X-RAY DIFFRACTION16{ B|104 - B|164 }B104 - 164
17X-RAY DIFFRACTION17{ B|165 - B|182 }B165 - 182
18X-RAY DIFFRACTION18{ B|183 - B|189 }B183 - 189
19X-RAY DIFFRACTION19{ B|190 - B|265 }B190 - 265
20X-RAY DIFFRACTION20{ B|266 - B|308 }B266 - 308
21X-RAY DIFFRACTION21{ B|309 - B|349 }B309 - 349
22X-RAY DIFFRACTION22{ B|350 - B|423 }B350 - 423
23X-RAY DIFFRACTION23{ B|424 - B|431 }B424 - 431
24X-RAY DIFFRACTION24{ B|432 - B|450 }B432 - 450
25X-RAY DIFFRACTION25{ C|14 - C|37 }C14 - 37
26X-RAY DIFFRACTION26{ C|38 - C|89 }C38 - 89
27X-RAY DIFFRACTION27{ C|90 - C|104 }C90 - 104
28X-RAY DIFFRACTION28{ C|105 - C|228 }C105 - 228
29X-RAY DIFFRACTION29{ C|229 - C|257 }C229 - 257
30X-RAY DIFFRACTION30{ C|258 - C|270 }C258 - 270
31X-RAY DIFFRACTION31{ C|271 - C|289 }C271 - 289
32X-RAY DIFFRACTION32{ C|290 - C|332 }C290 - 332
33X-RAY DIFFRACTION33{ C|333 - C|344 }C333 - 344
34X-RAY DIFFRACTION34{ C|345 - C|379 }C345 - 379
35X-RAY DIFFRACTION35{ C|380 - C|423 }C380 - 423
36X-RAY DIFFRACTION36{ C|424 - C|449 }C424 - 449
37X-RAY DIFFRACTION37{ D|14 - D|59 }D14 - 59
38X-RAY DIFFRACTION38{ D|60 - D|88 }D60 - 88
39X-RAY DIFFRACTION39{ D|89 - D|103 }D89 - 103
40X-RAY DIFFRACTION40{ D|104 - D|157 }D104 - 157
41X-RAY DIFFRACTION41{ D|158 - D|171 }D158 - 171
42X-RAY DIFFRACTION42{ D|172 - D|252 }D172 - 252
43X-RAY DIFFRACTION43{ D|253 - D|269 }D253 - 269
44X-RAY DIFFRACTION44{ D|270 - D|290 }D270 - 290
45X-RAY DIFFRACTION45{ D|291 - D|310 }D291 - 310
46X-RAY DIFFRACTION46{ D|311 - D|350 }D311 - 350
47X-RAY DIFFRACTION47{ D|351 - D|441 }D351 - 441
48X-RAY DIFFRACTION48{ D|442 - D|450 }D442 - 450
49X-RAY DIFFRACTION49{ A|801 }A801
50X-RAY DIFFRACTION50{ B|801 }B801
51X-RAY DIFFRACTION51{ C|801 }C801
52X-RAY DIFFRACTION52{ D|801 }D801

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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