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- PDB-9ev5: Corynebacterium glutamicum CS176 pyruvate:quinone oxidoreductase ... -

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基本情報

登録情報
データベース: PDB / ID: 9ev5
タイトルCorynebacterium glutamicum CS176 pyruvate:quinone oxidoreductase (PQO) in complex with FAD and thiamine diphosphate-magnesium ion
要素Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
キーワードOXIDOREDUCTASE / Pyruvate:quinone oxidoreductase / pyruvate / carbon metabolism
機能・相同性
機能・相同性情報


thiamine pyrophosphate binding / catalytic activity / magnesium ion binding
類似検索 - 分子機能
: / : / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
類似検索 - ドメイン・相同性
FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
類似検索 - 構成要素
生物種Corynebacterium glutamicum (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.863 Å
データ登録者Da Silva Lameira, C. / Muenssinger, S. / Yang, L. / Eikmanns, B.J. / Bellinzoni, M.
資金援助 フランス, 1件
組織認可番号
Agence Nationale de la Recherche (ANR)ANR-18-CE92-0003 フランス
引用ジャーナル: Febs J. / : 2024
タイトル: Corynebacterium glutamicum pyruvate:quinone oxidoreductase: an enigmatic metabolic enzyme with unusual structural features.
著者: da Silva Lameira, C. / Munssinger, S. / Yang, L. / Eikmanns, B.J. / Bellinzoni, M.
履歴
登録2024年3月28日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年8月7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: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
B: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
C: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
D: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)253,41416
ポリマ-248,4734
非ポリマー4,94112
25,6711425
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: native gel electrophoresis, Homotetrameric enzyme (Schreiner and Eikmanns, J. Bacteriol. 187: 862-871, 2005)
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area33030 Å2
ΔGint-238 kcal/mol
Surface area63430 Å2
単位格子
Length a, b, c (Å)104.192, 77.935, 158.044
Angle α, β, γ (deg.)90, 100.63, 90
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] / pyruvate:quinone oxidoreductase


分子量: 62118.246 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Corynebacterium glutamicum (バクテリア)
: CS176 / 遺伝子: Cgl2610 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q8NMG5, pyruvate dehydrogenase (quinone)
#2: 化合物
ChemComp-TPP / THIAMINE DIPHOSPHATE / 3-[(4-アミノ-2-メチル-5-ピリミジニル)メチル]-4-メチル-5-[2-(ホスホノオキシホスフィナトオキシ)(以下略)


分子量: 425.314 Da / 分子数: 4 / 由来タイプ: 合成 / : C12H19N4O7P2S / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / : Mg / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 4 / 由来タイプ: 合成 / : C27H33N9O15P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: FAD*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1425 / 由来タイプ: 天然 / : 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: 2.55 Å3/Da / 溶媒含有率: 51.69 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 / 詳細: 1.6 M tri-sodium citrate, pH 6.5

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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: 0.9763 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2021年7月3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: 0.9763 Å / 相対比: 1
反射解像度: 1.863→155.33 Å / Num. obs: 134984 / % 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: 0.99 / CC1/2 anomalous: -0.494 / Rmerge(I) obs: 0.2038 / Rpim(I) all: 0.0826 / Rrim(I) all: 0.2201 / AbsDiff over sigma anomalous: 0.652 / Baniso tensor eigenvalue 1: 0 Å2 / Baniso tensor eigenvalue 2: 10.6944 Å2 / Baniso tensor eigenvalue 3: 25.976 Å2 / Baniso tensor eigenvector 1 ortho1: 0.7702 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.6377 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.6377 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.7702 / Aniso diffraction limit 1: 1.849 Å / Aniso diffraction limit 2: 2.03 Å / Aniso diffraction limit 3: 2.539 Å / Aniso diffraction limit axis 1 ortho1: 0.75693 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.65353 / 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: -0.65353 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.75693 / Net I/σ(I): 5.83 / Num. measured all: 950618 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.5 / % possible ellipsoidal: 94.7 / % possible ellipsoidal anomalous: 94.5 / % possible spherical: 64.9 / % possible spherical anomalous: 64.6 / Redundancy anomalous: 3.59 / 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
5.912-155.337.120.083612.754805848058674967490.993-0.7070.03380.09030.3491001001001001003.76100
4.677-5.9126.850.104511.774620246202674967490.991-0.6420.04250.11290.4311001001001001003.54100
4.077-4.6766.860.110911.714628346283675067500.989-0.6240.04570.12010.4621001001001001003.52100
3.7-4.0776.750.129810.654557645576674967490.982-0.5540.05370.14070.52699.910099.910099.93.47100
3.433-3.77.110.14849.814795747957674967490.983-0.5970.05980.16010.54599.810099.810099.83.63100
3.228-3.4337.210.17428.684864048640674967490.975-0.510.06990.18790.60199.810099.810099.83.68100
3.065-3.2287.290.2167.524921049210674967490.961-0.4970.08620.23280.64599.810099.810099.83.72100
2.93-3.0657.340.26636.294957849578675067500.957-0.3790.10570.28680.6661001001001001003.74100
2.816-2.937.330.33465.444949049490674967490.938-0.2220.13260.36020.6999.710099.710099.73.74100
2.718-2.8166.60.40494.424451044510674967490.911-0.1580.17020.43980.71599.810099.810099.83.36100
2.632-2.7186.870.48263.954635346353674967490.902-0.1380.19840.52240.71899.499.599.499.599.43.4999.5
2.554-2.6327.110.55393.624795447954674967490.879-0.1110.22310.59770.7239897.89897.8983.6197.8
2.482-2.5547.150.60673.374824448244675067500.871-0.1440.24360.65460.7394.694.794.692.492.63.6394.7
2.41-2.4827.160.65993.114832948329674967490.839-0.1230.26470.71180.73592.392.592.38484.33.6492.5
2.341-2.416.710.73072.754529745297674967490.824-0.0810.30410.79260.7459292.39276.877.13.492.3
2.274-2.3416.740.76462.674548645486674967490.772-0.1020.31730.82890.72394.294.394.271.571.93.4194.3
2.21-2.2746.940.82472.514682246822674967490.77-0.0950.33690.89230.74995.595.895.565.465.63.5295.8
2.142-2.2097.090.98042.174783447834675067500.705-0.0770.39511.05820.74890.590.890.555.655.73.5990.8
2.064-2.1427.271.17351.864906749067674967490.655-0.0410.46621.26380.74983.784.183.742.342.33.6984.1
1.863-2.0647.371.36131.594972849728674967490.563-0.0460.53821.46470.75266.666.466.612.312.23.7466.4

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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 20221121data processing
Aimless0.7.9データスケーリング
autoPROC2.3.90data 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
開始モデル: 9EV3
解像度: 1.863→155.33 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.249 / 交差検証法: THROUGHOUT / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.192
Rfactor反射数%反射Selection details
Rfree0.2395 6723 -RANDOM
Rwork0.2068 ---
obs0.2085 134984 64.9 %-
原子変位パラメータBiso mean: 32.83 Å2
Baniso -1Baniso -2Baniso -3
1-7.54 Å20 Å2-4.2983 Å2
2---1.2832 Å20 Å2
3----6.2568 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
精密化ステップサイクル: LAST / 解像度: 1.863→155.33 Å
タンパク質核酸リガンド溶媒全体
原子数17098 0 320 1425 18843
拘束条件
Refine-IDタイプDev idealRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00817766HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9524225HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5952SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3124HARMONIC5
X-RAY DIFFRACTIONt_it17766HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2396SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact16454SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion16.51
LS精密化 シェル解像度: 1.863→2 Å
Rfactor反射数%反射
Rfree0.2708 125 -
Rwork0.2573 --
obs--6.91 %
精密化 TLS

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)
11.1141-0.16410.13070.7383-0.16270.7204-0.02540.1139-0.06440.11390.0078-0.0371-0.0644-0.03710.01750.15220.0105-0.0957-0.0787-0.0162-0.094721.278520.081257.2174
23.02321.1422-1.14543.9093-2.28782.72380.03480.0223-0.07670.02230.0052-0.2127-0.0767-0.2127-0.040.10290.0199-0.0778-0.0431-0.016-0.149610.914320.864455.3019
31.3384-0.576-0.04290.9179-0.26960.6186-0.14220.22630.11520.22630.1457-0.20260.1152-0.2026-0.00350.0733-0.0305-0.0219-0.08480.0324-0.02038.9801-9.152963.9645
42.857-1.31410.41071.3014-0.00930.9987-0.060.00360.22940.00360.0452-0.15560.2294-0.15560.01470.1078-0.07-0.0421-0.14890.01530.117611.6291-17.418756.7367
51.2746-1.3771-0.04031.4501-0.0256-0.0287-0.04970.28730.12850.28730.06040.18280.12850.1828-0.01070.22090.0401-0.1047-0.16820.1088-0.054534.707-20.440368.69
60.406-0.04510.23680.8087-0.18010.62370.0180.17360.03180.1736-0.02440.06440.03180.06440.00640.16380.0002-0.1256-0.08130.0356-0.063837.47160.406466.029
70.5723-0.156-0.20751.0366-0.00421.1695-0.0003-0.02730.0943-0.02730.0521-0.02080.0943-0.0208-0.05180.10040.0153-0.086-0.16070.0706-0.038334.0827-14.533361.0634
81.73570.31270.12841.8480.18141.98250.0336-0.07350.1671-0.07350.00140.17910.16710.1791-0.0350.10920.0282-0.071-0.0692-0.0211-0.089344.53813.85438.2083
91.43190.6178-0.09170.74570.05790.5436-0.0364-0.11460.0064-0.11460.0197-0.04230.0064-0.04230.01670.13570.0023-0.0761-0.0463-0.0235-0.099931.88586.704836.2872
101.068-0.06510.11275.13590.62711.5090.0246-0.3175-0.0942-0.3175-0.07180.093-0.09420.0930.0472-0.0063-0.02910.02740.05090.0508-0.298636.953624.037218.5128
111.8516-0.0080.45021.2250.00742.2785-0.0051-0.2215-0.3404-0.22150.00760.0958-0.34040.0958-0.00250.17-0.0073-0.0188-0.1040.0857-0.05139.372442.890129.7156
120.6260.635-0.44340.35010.09432.1539-0.01060.3111-0.6360.31110.05760.2206-0.6360.2206-0.0470.1497-0.0894-0.094-0.1916-0.04190.102950.210946.540950.4655
130.6325-0.2367-0.06750.70130.0210.34970.02080.0696-0.1250.0696-0.0220.1498-0.1250.14980.00120.1339-0.0338-0.1171-0.0823-0.0001-0.024546.70825.183353.2639
140.9503-0.3433-0.14441.0717-0.10160.8569-0.03060.1279-0.27350.12790.03390.1399-0.27350.1399-0.00330.1275-0.0842-0.1166-0.1532-0.0104-0.021346.75139.184851.9247
151.0730.0873-0.13210.7642-0.10460.8171-0.0186-0.18190.0942-0.1819-0.011-0.25850.0942-0.25850.02960.068-0.0376-0.12840.1011-0.1225-0.10245.9394-1.497928.7749
161.91180.2312-0.86291.2166-0.29293.2941-0.0845-0.0210.2826-0.0210.0284-0.27840.2826-0.27840.05610.0827-0.0417-0.1047-0.0252-0.0736-0.084711.1387-6.205936.5938
171.892-0.8043-0.93390.99990.64631.716-0.0073-0.0338-0.0391-0.0338-0.0606-0.3142-0.0391-0.31420.06790.0201-0.0484-0.0904-0.07860.0339-0.05240.5514-3.330555.6721
182.2551-0.65150.36621.7031-0.43861.92090.01130.1216-0.08390.12160.0189-0.3435-0.0839-0.3435-0.0302-0.0020.0262-0.04260.0376-0.0147-0.1053-14.232112.772358.2239
191.703-0.0255-0.99030.80550.32921.8314-0.0099-0.0829-0.1898-0.08290.0278-0.4901-0.1898-0.4901-0.0179-0.09820.0748-0.13950.1777-0.0196-0.1001-25.915317.286940.1494
201.33440.02190.02990.9211-0.14020.79980.0403-0.143-0.0368-0.143-0.0337-0.5299-0.0368-0.5299-0.0066-0.03990.0183-0.19270.3248-0.0607-0.1812-15.898513.542225.0578
211.5727-0.0928-0.35440-0.14080.69010.09990.0229-0.03460.0229-0.012-0.2883-0.0346-0.2883-0.0879-0.00190.1084-0.14820.03360.0166-0.1278-20.887121.986540.4267
222.39610.579-0.20441.72080.75011.6048-0.0157-0.1591-0.2398-0.15910.0302-0.305-0.2398-0.305-0.01450.07850.1054-0.14330.110.1084-0.2434.1932.240823.092
230.6547-0.04440.02880.33780.4520.75180.0418-0.0943-0.0006-0.09430.0251-0.1998-0.0006-0.1998-0.06690.09880.0249-0.10140.09020.0196-0.18719.600321.95231.2181
243.68082.5142-0.74120.7264-2.40461.8587-0.024-0.0024-0.1257-0.00240.0305-0.1614-0.1257-0.1614-0.00650.12080.0439-0.1177-0.00450.0589-0.148715.358131.769431.4111
252.291-1.684-1.63332.1021.50672.18510.1842-0.2327-0.2559-0.2327-0.0932-0.1069-0.2559-0.1069-0.0910.0957-0.0082-0.06490.01790.0792-0.208632.965428.874118.4301
262.69350.4231-0.14711.61930.21961.9784-0.0319-0.3910.0701-0.391-0.0295-0.01480.0701-0.01480.06140.1232-0.0026-0.01370.2655-0.0477-0.318833.621512.47623.6883
273.32751.0471.27550.9971-0.62140.36160.0028-0.4757-0.0613-0.47570.0236-0.0424-0.0613-0.0424-0.02640.0894-0.0312-0.1310.5343-0.3142-0.460615.77493.2949-8.8908
281.1599-0.40560.88541.72710.51161.48920.0554-0.27950.0572-0.2795-0.0596-0.10070.0572-0.10070.00410.05010.0452-0.14460.3977-0.0076-0.346910.133717.05774.6238
290.02281.399-0.17440.3679-0.1781.21240.1596-0.21370.1305-0.2137-0.0857-0.34750.1305-0.3475-0.07390.01920.0279-0.2330.3726-0.1158-0.35051.051210.328.8837
302.3758-0.05360.72251.5024-0.08413.43560.0923-0.24030.1129-0.24030.0282-0.04280.1129-0.0428-0.1206-0.1048-0.009-0.19560.4668-0.2688-0.4456-2.00076.121.4325
313.75390.6454-1.36341.6623-0.93654.32050.0688-0.37310.397-0.37310.03010.14180.3970.1418-0.0989-0.05570.0188-0.09520.3198-0.3388-0.531523.24262.4255-2.1607
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - 132 }A2 - 132
2X-RAY DIFFRACTION2{ A|133 - 164 }A133 - 164
3X-RAY DIFFRACTION3{ A|165 - 250 }A165 - 250
4X-RAY DIFFRACTION4{ A|251 - 328 }A251 - 328
5X-RAY DIFFRACTION5{ A|329 - 371 }A329 - 371
6X-RAY DIFFRACTION6{ A|372 - 519 }A372 - 519
7X-RAY DIFFRACTION7{ A|520 - 576 }A520 - 576
8X-RAY DIFFRACTION8{ B|2 - 63 }B2 - 63
9X-RAY DIFFRACTION9{ B|64 - 164 }B64 - 164
10X-RAY DIFFRACTION10{ B|165 - 200 }B165 - 200
11X-RAY DIFFRACTION11{ B|201 - 328 }B201 - 328
12X-RAY DIFFRACTION12{ B|329 - 371 }B329 - 371
13X-RAY DIFFRACTION13{ B|372 - 506 }B372 - 506
14X-RAY DIFFRACTION14{ B|507 - 577 }B507 - 577
15X-RAY DIFFRACTION15{ C|2 - 132 }C2 - 132
16X-RAY DIFFRACTION16{ C|133 - 164 }C133 - 164
17X-RAY DIFFRACTION17{ C|165 - 200 }C165 - 200
18X-RAY DIFFRACTION18{ C|201 - 328 }C201 - 328
19X-RAY DIFFRACTION19{ C|329 - 400 }C329 - 400
20X-RAY DIFFRACTION20{ C|401 - 519 }C401 - 519
21X-RAY DIFFRACTION21{ C|520 - 577 }C520 - 577
22X-RAY DIFFRACTION22{ D|2 - 63 }D2 - 63
23X-RAY DIFFRACTION23{ D|64 - 132 }D64 - 132
24X-RAY DIFFRACTION24{ D|133 - 164 }D133 - 164
25X-RAY DIFFRACTION25{ D|165 - 200 }D165 - 200
26X-RAY DIFFRACTION26{ D|201 - 328 }D201 - 328
27X-RAY DIFFRACTION27{ D|329 - 371 }D329 - 371
28X-RAY DIFFRACTION28{ D|372 - 429 }D372 - 429
29X-RAY DIFFRACTION29{ D|430 - 476 }D430 - 476
30X-RAY DIFFRACTION30{ D|477 - 542 }D477 - 542
31X-RAY DIFFRACTION31{ D|543 - 577 }D543 - 577

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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