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- PDB-8ar7: Bovine glutamate dehydrogenase in ternary complex with the allost... -

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基本情報

登録情報
データベース: PDB / ID: 8ar7
タイトルBovine glutamate dehydrogenase in ternary complex with the allosteric activators ADP and leucine
要素Glutamate dehydrogenase (NAD(P)(+))
キーワードCYTOSOLIC PROTEIN / Glutamate dehydrogenase / allosteric regulator / ADP / Leucine
機能・相同性
機能・相同性情報


Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation / positive regulation of insulin secretion / mitochondrial matrix ...Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation / positive regulation of insulin secretion / mitochondrial matrix / nucleotide binding / mitochondrion
類似検索 - 分子機能
NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / : / LEUCINE / Glutamate dehydrogenase 1, mitochondrial
類似検索 - 構成要素
生物種Bos taurus (ウシ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.448 Å
データ登録者Aleshin, V.A. / Bellinzoni, M.
資金援助 フランス, 1件
組織認可番号国
Pasteur Institute フランス
引用
ジャーナル: Int J Mol Sci / 年: 2022
タイトル: Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase.
著者: Aleshin, V.A. / Bunik, V.I. / Bruch, E.M. / Bellinzoni, M.
#1: ジャーナル: Preprints / 年: 2022
タイトル: Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase
著者: Aleshin, V.A. / Bunik, V.I. / Bruch, E.M. / Bellinzoni, M.
履歴
登録2022年8月15日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年10月5日Provider: repository / タイプ: Initial release
改定 1.12022年10月26日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Glutamate dehydrogenase (NAD(P)(+))
B: Glutamate dehydrogenase (NAD(P)(+))
C: Glutamate dehydrogenase (NAD(P)(+))
D: Glutamate dehydrogenase (NAD(P)(+))
E: Glutamate dehydrogenase (NAD(P)(+))
F: Glutamate dehydrogenase (NAD(P)(+))
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)373,87624
ポリマ－370,2916
非ポリマー3,58518
水7,909439
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: homology
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area41910 Å2
ΔGint-175 kcal/mol
Surface area98580 Å2
手法PISA
単位格子
Length a, b, c (Å)90.877, 178.705, 123.884
Angle α, β, γ (deg.)90, 104, 90
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Glutamate dehydrogenase (NAD(P)(+))


分子量: 61715.160 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: A0A140T871, glutamate dehydrogenase [NAD(P)+]
#2: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: ADP, エネルギー貯蔵分子*YM
#3: 化合物
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 6 / 由来タイプ: 合成 / 式: K
#4: 化合物
ChemComp-LEU / LEUCINE / ロイシン


タイプ: L-peptide linking / 分子量: 131.173 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C6H13NO2 / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 439 / 由来タイプ: 天然 / 式: H2O
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: 2.64 Å3/Da / 溶媒含有率: 53.34 %
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: 7 / 詳細: 20% EtOH, 30% 2-methyl-2,4-pentanediol (MPD)

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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: ESRF / ビームライン: ID30B / 波長: 0.97625 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年3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: 0.97625 Å / 相対比: 1
反射解像度: 2.448→120.203 Å / Num. obs: 82997 / % possible obs: 92 % / 冗長度: 5.37 %
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: 0.989 / CC1/2 anomalous: -0.026 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.0945 / Rrim(I) all: 0.2201 / AbsDiff over sigma anomalous: 0.773 / Baniso tensor eigenvalue 1: 14.7539 Å2 / Baniso tensor eigenvalue 2: 35.9606 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9732 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.2301 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.2301 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9732 / Aniso diffraction limit 1: 3.035 Å / Aniso diffraction limit 2: 3.121 Å / Aniso diffraction limit 3: 2.448 Å / Aniso diffraction limit axis 1 ortho1: 0.94808 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.31799 / 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: -0.31799 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.94808 / Net I/σ(I): 6.82 / Num. measured all: 445692 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91.4 / % possible ellipsoidal: 92 / % possible ellipsoidal anomalous: 91.4 / % possible spherical: 59 / % possible spherical anomalous: 58.3 / Redundancy anomalous: 2.74 / 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
7.931-120.2034.910.077316.12039720397415041500.9920.0530.03830.08680.7279797.99797.9972.5897.9
6.296-7.9315.130.100213.152127121271415041500.987-0.0380.04830.11170.78898.599.398.599.398.52.6499.3
5.488-6.2965.130.121710.992129721297414941490.983-0.1310.05910.13590.77596.197.696.197.696.12.6497.6
4.985-5.4885.440.127911.082256922569415041500.983-0.1510.06040.14190.78998.499.498.499.498.42.7999.4
4.628-4.9855.430.116211.732252922529415041500.986-0.0420.05480.12890.77498.899.398.899.398.82.7799.3
4.354-4.6285.30.128910.972200322003414941490.983-0.1240.06190.14350.77898.899.398.899.398.82.799.3
4.134-4.3545.340.15589.492216122161415141510.977-0.0630.07440.17320.7797.298.297.298.297.22.7398.2
3.954-4.1345.330.18388.422211522115415041500.971-0.0740.0880.20440.78498.899.198.899.198.82.7199.1
3.801-3.9545.510.22677.522288622886415041500.965-0.0950.10660.25130.76598.69998.69998.62.899
3.67-3.8015.560.27366.522307623076414941490.96-0.0330.12810.30290.77298.899.198.899.198.82.8299.1
3.555-3.675.60.35855.462322723227415041500.933-0.0490.16720.39660.78498.89998.89998.82.8499
3.453-3.5555.360.45314.462225022250415041500.8950.0090.21670.5040.77798.69998.69998.62.7299
3.362-3.4535.40.55453.782239822398414941490.848-0.0230.26410.61610.77898.298.998.298.998.22.7498.9
3.279-3.3625.510.69983.212285022850414941490.773-0.0270.32870.77540.75898.198.898.198.898.12.898.8
3.203-3.2795.270.82652.642189421894415241520.69500.39850.92070.78996.497.596.497.596.42.6997.5
3.13-3.2035.30.88652.352201322013415041500.676-0.0190.42660.9870.76991.792.291.792.291.72.6992.2
3.047-3.135.290.8622.422192421924414741470.6070.0040.41630.96030.7679.480.279.473.472.62.6980.2
2.947-3.0475.321.02242.132209222092415141510.52-0.070.48981.13710.76279.980.879.954.253.22.7280.8
2.793-2.9475.540.95792.282298322983415041500.544-0.0540.44691.05960.77469.869.969.829.4292.8269.9
2.448-2.7935.721.21131.782375723757415141510.407-0.0810.55111.33310.7926160.9619.18.92.9160.9

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解析

ソフトウェア
名称バージョン分類
BUSTER2.10.4 (8-JUN-2022)精密化
autoPROCデータ削減
STARANISOデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3JCZ

3jcz


解像度: 2.448→120.2 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.927 / 交差検証法: THROUGHOUT / SU Rfree Blow DPI: 0.322
Rfactor反射数%反射Selection details
Rfree0.2145 4196 -RANDOM
Rwork0.1919 ---
obs0.193 82997 59 %-
原子変位パラメータBiso mean: 68.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.782 Å20 Å20.7712 Å2
2--1.2819 Å20 Å2
3----2.064 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
精密化ステップサイクル: LAST / 解像度: 2.448→120.2 Å
タンパク質核酸リガンド溶媒全体
原子数22994 0 222 439 23655
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00623708HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7532098HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10896SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4077HARMONIC5
X-RAY DIFFRACTIONt_it23708HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3114SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact19680SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion2.69
LS精密化 シェル解像度: 2.45→2.65 Å
Rfactor反射数%反射
Rfree0.3145 81 -
Rwork0.2964 --
obs0.2972 1660 5.63 %
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)
12.2232-0.6522-0.86173.56180.41312.4736-0.1882-0.04470.3433-0.04470.1277-0.37180.3433-0.37180.06040.0182-0.08320.0023-0.0121-0.0253-0.1046-4.422716.974224.6825
23.50120.5480.34557.9152-1.02223.7498-0.1968-1.55880.8553-1.55880.5203-0.60730.8553-0.6073-0.32350.058-0.2302-0.32890.16170.0273-0.0162-6.955711.2823-1.0094
33.3719-3.3113-0.95183.26483.27288.10460.3464-0.6294-0.4783-0.6294-0.27860.6577-0.47830.6577-0.06780.10280.0450.05180.06340.0647-0.166725.956127.5937-7.2632
42.93581.2382-0.23486.65151.36482.3018-0.1944-0.47081.2848-0.47080.0656-0.17561.2848-0.17560.1289-0.01780.00640.0828-0.1501-0.1682-0.03487.19243.869814.3063
52.75090.5092-0.54351.7584-0.03442.1906-0.03310.33740.52270.33740.01650.53810.52270.53810.0166-0.03950.2356-0.03120.0589-0.0466-0.136131.340716.423438.4353
67.8658-0.08180.09983.55260.62382.81910.1280.06990.82220.06990.16370.62650.82220.6265-0.29170.07430.2904-0.02780.022-0.06060.06245.96463.42420.3173
73.55061.3611-2.67891.0923-3.72041.3805-0.1483-0.60021.1269-0.6002-0.0752-0.23491.1269-0.23490.22340.34480.18470.0590.0576-0.0598-0.125122.893415.5897-6.1452
87.3561-1.0398-1.38661.45810.04681.6105-0.1614-0.10910.0395-0.10910.59321.22760.03951.2276-0.4319-0.18780.12230.02580.15910.0563-0.165242.704625.060223.8068
93.0612-0.85770.36382.0050.05373.79740.0322-0.0975-0.3422-0.09750.03740.044-0.34220.044-0.0695-0.0733-0.02570.0672-0.09190.0104-0.063616.011149.423426.3402
104.736-0.5415-0.05314.6867-1.82763.9837-0.0166-0.0329-0.8054-0.0329-0.26480.4922-0.80540.49220.28140.0563-0.09450.1135-0.09270.09020.315229.140456.00984.4146
112.12170.9827-0.0042.80941.760810.90720.0376-0.36840.6945-0.3684-0.05831.30860.69451.30860.02070.00360.27390.11250.12420.1199-0.066234.041819.5169-2.5595
12-0.7073-1.29522.11965.7244-2.96034.66070.3777-0.5847-0.432-0.5847-0.0683-0.3955-0.432-0.3955-0.3093-0.01180.0176-0.0249-0.1064-0.0468-0.15899.732445.72917.3297
132.15850.0491-0.69383.1701-0.40563.1265-0.22860.13610.25630.13610.18380.5710.25630.5710.0448-0.09950.2252-0.05790.1063-0.0546-0.170125.126923.831559.7373
141.9321-0.63920.3344.7858-0.4714.2038-0.20540.777-0.03560.7770.10461.0003-0.03561.00030.1008-0.12010.2747-0.21770.4421-0.1370.032228.192328.038885.4276
153.62441.51-3.09662.2175-0.89237.88760.16490.7113-1.06420.7113-0.02390.0414-1.06420.0414-0.1410.25980.2195-0.0277-0.0157-0.0708-0.1791-5.479745.033285.517
161.7214-1.66710.86182.8925-0.8263.0185-0.29160.52180.64030.52180.29950.23970.64030.2397-0.00790.00250.21730.08570.04920.1006-0.08313.812215.637175.0367
172.8587-1.12630.03122.25750.16862.1307-0.0178-0.10630.5609-0.1063-0.002-0.25460.5609-0.25460.01980.0251-0.0530.0419-0.05630.0134-0.0698-10.922717.506247.3478
184.19521.03-0.08042.862-0.3152.2760.00190.31780.43760.31780.0966-0.30240.4376-0.3024-0.09860.10350.00820.0853-0.10010.047-0.0228-25.263112.418469.1475
193.598-2.4897-5.42527.284.798911.1184-0.25980.75530.05090.75530.22460.92020.05090.92020.03520.07430.1541-0.05010.11860.0502-0.1781-2.22333.626289.0057
206.4318-0.1509-0.61361.86820.12910.6164-0.15690.162-0.01940.1620.288-0.7945-0.0194-0.7945-0.1311-0.11690.04710.0506-0.11110.01260.0282-22.178731.138257.6174
212.21440.63630.22931.76610.30853.2141-0.0178-0.0367-0.4374-0.03670.14620.1101-0.43740.1101-0.12840.00310.05910.0295-0.0759-0.03260.02224.162553.50846.3105
222.3796-0.1564-0.3776.62850.26351.86590.07360.3445-0.43310.34450.1884-0.1695-0.4331-0.1695-0.2620.06420.14580.0747-0.11580.0056-0.0178-8.970866.834665.201
23-0.2301-0.6031-0.09552.0970.490712.62410.05070.4234-0.07210.42340.057-0.7921-0.0721-0.7921-0.10770.05850.14410.07930.0723-0.0261-0.0413-13.548235.715684.2805
242.29722.09410.58465.48781.25842.17660.19340.3496-0.35680.34960.00570.3117-0.35680.3117-0.19920.06160.029-0.104-0.1023-0.0313-0.077410.664156.635165.4057
25-1.4016-2.08382.63012.4532-0.86151.44350.1208-0.21010.0406-0.2101-0.37620.46110.04060.46110.25540.30440.07740.0620.09970.0237-0.24912.40678.715718.5833
263.0193-5.81540.70610-1.57810.1644-0.2194-1.2994-0.3004-1.29940.19770.3752-0.30040.37520.02170.2390.1634-0.05890.1393-0.1294-0.038335.315928.747723.604
273.3127-3.6269-6.19812.1481-5.3918-3.29750.2696-0.13410.0897-0.13410.1930.58110.08970.5811-0.46260.18030.08160.27380.26430.1185-0.00758.800438.628411.5031
28-3.3862-7.60216.447201.9763.44510.02830.58110.0180.5811-0.215-0.14470.018-0.14470.18670.39420.2271-0.17280.0279-0.0843-0.15098.46218.251468.6038
293.27190.3094-3.78584.2061-4.92621.0417-0.07611.2114-0.62321.2114-0.08710.2592-0.62320.25920.1632-0.00290.0004-0.03120.19570.1859-0.0993-14.798134.72556.453
30-1.4156-2.52932.66160.1163-1.98951.41560.11910.21470.04340.21470.02980.07620.04340.0762-0.14890.00840.16940.01240.0186-0.10930.112311.731748.579163.945
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|65 - A|270 A|701 }A65 - 270
2X-RAY DIFFRACTION1{ A|65 - A|270 A|701 }A701
3X-RAY DIFFRACTION2{ A|271 - A|451 }A271 - 451
4X-RAY DIFFRACTION3{ A|452 - A|505 }A452 - 505
5X-RAY DIFFRACTION4{ A|506 - A|560 A|661 }A506 - 560
6X-RAY DIFFRACTION4{ A|506 - A|560 A|661 }A661
7X-RAY DIFFRACTION5{ B|64 - B|270 B|701 }B64 - 270
8X-RAY DIFFRACTION5{ B|64 - B|270 B|701 }B701
9X-RAY DIFFRACTION6{ B|271 - B|451 }B271 - 451
10X-RAY DIFFRACTION7{ B|452 - B|505 }B452 - 505
11X-RAY DIFFRACTION8{ B|506 - B|560 B|661 }B506 - 560
12X-RAY DIFFRACTION8{ B|506 - B|560 B|661 }B661
13X-RAY DIFFRACTION9{ C|67 - C|270 C|701 }C67 - 270
14X-RAY DIFFRACTION9{ C|67 - C|270 C|701 }C701
15X-RAY DIFFRACTION10{ C|271 - C|451 }C271 - 451
16X-RAY DIFFRACTION11{ C|452 - C|505 }C452 - 505
17X-RAY DIFFRACTION12{ C|506 - C|560 C|661 }C506 - 560
18X-RAY DIFFRACTION12{ C|506 - C|560 C|661 }C661
19X-RAY DIFFRACTION13{ D|64 - D|270 D|701 }D64 - 270
20X-RAY DIFFRACTION13{ D|64 - D|270 D|701 }D701
21X-RAY DIFFRACTION14{ D|271 - D|451 }D271 - 451
22X-RAY DIFFRACTION15{ D|452 - D|505 }D452 - 505
23X-RAY DIFFRACTION16{ D|506 - D|560 D|661 }D506 - 560
24X-RAY DIFFRACTION16{ D|506 - D|560 D|661 }D661
25X-RAY DIFFRACTION17{ E|62 - E|270 E|701 }E62 - 270
26X-RAY DIFFRACTION17{ E|62 - E|270 E|701 }E701
27X-RAY DIFFRACTION18{ E|271 - E|451 }E271 - 451
28X-RAY DIFFRACTION19{ E|452 - E|505 }E452 - 505
29X-RAY DIFFRACTION20{ E|506 - E|560 E|661 }E506 - 560
30X-RAY DIFFRACTION20{ E|506 - E|560 E|661 }E661
31X-RAY DIFFRACTION21{ F|62 - F|270 F|701 }F62 - 270
32X-RAY DIFFRACTION21{ F|62 - F|270 F|701 }F701
33X-RAY DIFFRACTION22{ F|271 - F|451 }F271 - 451
34X-RAY DIFFRACTION23{ F|452 - F|505 }F452 - 505
35X-RAY DIFFRACTION24{ F|506 - F|560 F|661 }F506 - 560
36X-RAY DIFFRACTION24{ F|506 - F|560 F|661 }F661
37X-RAY DIFFRACTION25{ A|601 }A601
38X-RAY DIFFRACTION26{ B|601 }B601
39X-RAY DIFFRACTION27{ C|601 }C601
40X-RAY DIFFRACTION28{ D|602 }D602
41X-RAY DIFFRACTION29{ E|602 }E602
42X-RAY DIFFRACTION30{ F|601 }F601

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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