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- PDB-4is4: The glutamine synthetase from the dicotyledonous plant M. truncat... -

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基本情報

登録情報
データベース: PDB / ID: 4is4
タイトルThe glutamine synthetase from the dicotyledonous plant M. truncatula is a decamer
要素Glutamine synthetase
キーワードLIGASE / decamer dicotyledonous
機能・相同性
機能・相同性情報


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / cytoplasm
類似検索 - 分子機能
Glutamine synthetase, N-terminal domain / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily ...Glutamine synthetase, N-terminal domain / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Glutamine synthetase
類似検索 - 構成要素
生物種Medicago truncatula (タルウマゴヤシ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.35 Å
データ登録者Seabra, A.R. / Carvalho, H. / Pereira, P.J.B.
引用
ジャーナル: Acta Crystallogr D Biol Crystallogr / : 2014
タイトル: The structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture.
著者: Eva Torreira / Ana Rita Seabra / Hazel Marriott / Min Zhou / Óscar Llorca / Carol V Robinson / Helena G Carvalho / Carlos Fernández-Tornero / Pedro José Barbosa Pereira /
要旨: The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily ...The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily metabolizable glutamine, which in turn is at the basis of all subsequent biosynthesis of nitrogenous compounds. The essential role performed by glutamine synthetase makes it a prime target for herbicidal compounds, but also a suitable intervention point for the improvement of crop yields. Although the majority of crop plants are dicotyledonous, little is known about the structural organization of glutamine synthetase in these organisms and about the functional differences between the different isoforms. Here, the structural characterization of two glutamine synthetase isoforms from the model legume Medicago truncatula is reported: the crystallographic structure of cytoplasmic GSII-1a and an electron cryomicroscopy reconstruction of plastid-located GSII-2a. Together, these structural models unveil a decameric organization of dicotyledonous glutamine synthetase, with two pentameric rings weakly connected by inter-ring loops. Moreover, rearrangement of these dynamic loops changes the relative orientation of the rings, suggesting a zipper-like mechanism for their assembly into a decameric enzyme. Finally, the atomic structure of M. truncatula GSII-1a provides important insights into the structural determinants of herbicide resistance in this family of enzymes, opening new avenues for the development of herbicide-resistant plants.
#1: ジャーナル: Acta Crystallogr.,Sect.F / : 2009
タイトル: Crystallization and preliminary crystallographic characterization of glutamine synthetase from Medicago truncatula.
著者: Seabra, A.R. / Carvalho, H. / Pereira, P.J.
履歴
登録2013年1月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年4月9日Provider: repository / タイプ: Initial release
改定 1.12014年9月24日Group: Database references
改定 1.22023年9月20日Group: Data collection / Database references / 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase
G: Glutamine synthetase
H: Glutamine synthetase
I: Glutamine synthetase
J: Glutamine synthetase


分子量 (理論値)分子数
合計 (水以外)415,50410
ポリマ-415,50410
非ポリマー00
17,457969
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
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area36110 Å2
ΔGint-174 kcal/mol
Surface area119020 Å2
手法PISA
単位格子
Length a, b, c (Å)99.335, 101.672, 188.084
Angle α, β, γ (deg.)90.00, 103.69, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Glutamine synthetase


分子量: 41550.441 Da / 分子数: 10 / 由来タイプ: 組換発現
由来: (組換発現) Medicago truncatula (タルウマゴヤシ)
遺伝子: MTR_6g071070 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O04998, glutamine synthetase
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 969 / 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: 2.22 Å3/Da / 溶媒含有率: 44.62 %
結晶化温度: 287 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.4
詳細: 0.12 M triammonium citrate, 9.2% PEG3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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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: ESRF / ビームライン: ID14-2 / 波長: 0.933 Å
検出器タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2006年2月17日
放射モノクロメーター: Diamond (111), Ge(220) / 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: 0.933 Å / 相対比: 1
反射解像度: 2.35→101 Å / Num. all: 0 / Num. obs: 149655 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 6.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.2
反射 シェル解像度: 2.35→2.48 Å / 冗長度: 5.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4 / % possible all: 96.8

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解析

ソフトウェア
名称バージョン分類
ADSCQuantumデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.1_1168)精密化
MOSFLMデータ削減
SCALAデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 2D3A
解像度: 2.35→96.511 Å / SU ML: 0.26 / σ(F): 1.34 / 位相誤差: 23.09 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2166 7518 5.03 %RANDOM
Rwork0.1746 ---
obs0.1767 149449 98.69 %-
all-0 --
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.35→96.511 Å
タンパク質核酸リガンド溶媒全体
原子数23940 0 0 969 24909
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00824607
X-RAY DIFFRACTIONf_angle_d1.16533517
X-RAY DIFFRACTIONf_dihedral_angle_d12.7978995
X-RAY DIFFRACTIONf_chiral_restr0.073519
X-RAY DIFFRACTIONf_plane_restr0.0064365
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.3770.26692720.22394339X-RAY DIFFRACTION92
2.377-2.40490.27352450.21064633X-RAY DIFFRACTION97
2.4049-2.43430.26462460.1984658X-RAY DIFFRACTION98
2.4343-2.46510.23792480.19254675X-RAY DIFFRACTION98
2.4651-2.49750.26832600.19834688X-RAY DIFFRACTION98
2.4975-2.53170.27982470.19724741X-RAY DIFFRACTION99
2.5317-2.56790.25372500.19644697X-RAY DIFFRACTION99
2.5679-2.60620.2522540.18234740X-RAY DIFFRACTION99
2.6062-2.6470.23992530.18724676X-RAY DIFFRACTION99
2.647-2.69040.25822220.19564792X-RAY DIFFRACTION99
2.6904-2.73680.29222380.19634775X-RAY DIFFRACTION99
2.7368-2.78650.25252370.20114714X-RAY DIFFRACTION99
2.7865-2.84010.26522620.20074735X-RAY DIFFRACTION99
2.8401-2.89810.25552540.19394713X-RAY DIFFRACTION99
2.8981-2.96110.26882640.18864705X-RAY DIFFRACTION99
2.9611-3.030.25512560.19654760X-RAY DIFFRACTION99
3.03-3.10580.25552860.19314750X-RAY DIFFRACTION99
3.1058-3.18980.21542520.18264755X-RAY DIFFRACTION99
3.1898-3.28360.2362630.18784731X-RAY DIFFRACTION99
3.2836-3.38960.22752810.18664732X-RAY DIFFRACTION99
3.3896-3.51080.22092560.18664722X-RAY DIFFRACTION99
3.5108-3.65140.24552330.19544780X-RAY DIFFRACTION99
3.6514-3.81750.24012360.21654745X-RAY DIFFRACTION99
3.8175-4.01880.18122330.16094729X-RAY DIFFRACTION99
4.0188-4.27060.15732310.13734828X-RAY DIFFRACTION99
4.2706-4.60030.16712520.1214794X-RAY DIFFRACTION100
4.6003-5.06330.17172490.13254821X-RAY DIFFRACTION99
5.0633-5.79590.18172630.14234778X-RAY DIFFRACTION99
5.7959-7.30180.21342620.16854837X-RAY DIFFRACTION99
7.3018-96.59270.16082130.1714888X-RAY DIFFRACTION98
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)
17.90021.0281-5.66352.7222.6968.68080.7241-0.70741.2876-0.00120.2945-0.5679-0.9460.8513-0.8460.453-0.055-0.05080.46850.03780.470523.904419.7418-54.3885
23.0389-0.2656-0.26282.6834-0.36442.13260.09740.028-0.3131-0.2746-0.0928-0.08230.56430.19270.01330.39970.107-0.04320.1410.04350.274317.89665.7767-72.7124
30.5551-0.1475-0.17411.0617-0.20340.62440.20890.2118-0.0394-0.4166-0.1699-0.07740.34260.0984-0.02970.43020.1298-0.01380.19360.02510.289716.167413.574-82.5856
48.0718-1.5760.83067.1693-1.37463.59440.0282-0.6305-0.4593-0.32810.34391.52110.3647-0.7333-0.28440.1777-0.0283-0.01670.2235-0.01840.4424-10.202927.9135-70.0408
51.2585-0.6212-0.00971.8159-0.05550.51680.19740.0585-0.0235-0.0678-0.1373-0.02590.01950.0358-0.07740.2130.02350.00680.09470.02460.23048.225127.5649-74.4229
65.6253-1.0676-2.3483.24911.0433.5407-0.08150.8858-0.3556-0.5471-0.13231.0819-0.0891-0.66780.16140.2972-0.024-0.08970.2415-0.0310.4669-5.003322.1112-76.7388
75.52930.61150.07051.96680.31355.1090.34610.60430.1339-0.8762-0.1686-0.04010.36970.2603-0.14140.60770.1839-0.01630.30560.07050.339410.402223.3017-101.0041
85.99411.1173-0.19111.8904-2.09885.46560.2473-0.0169-0.32340.03340.17620.6843-0.0953-0.929-0.33040.551-0.0027-0.13310.43930.07490.5551-0.221325.5872-97.5983
91.7097-0.0170.24042.1349-1.5812.01380.29930.08280.3705-0.6695-0.10540.38130.1233-0.1748-0.08960.62060.1593-0.04530.16090.04940.38559.223421.987-95.6073
103.63251.4323.97479.674-2.84357.9163-0.23291.54361.7114-0.4829-0.2674-0.5443-0.29650.96050.42680.4918-0.10950.06720.51920.00260.399224.950727.9101-39.3861
111.5628-0.45410.76121.17490.31342.01810.165-0.0961-0.2390.15430.0206-0.06010.98710.703-0.06630.5370.1974-0.09210.31260.04250.350526.77081.6862-37.7397
123.44620.3850.73510.5631-0.14753.23960.1044-0.0865-0.2097-0.02310.05550.12550.4231-0.1688-0.15110.2679-0.0057-0.01220.10970.07040.279110.35877.2989-57.2904
131.4724-0.02860.2920.56190.0891.44850.146-0.2346-0.36460.13110.10010.16190.8594-0.0496-0.06850.4370.0296-0.090.11780.10220.302513.56623.0315-48.2661
141.8129-0.5002-0.51293.49140.70071.38510.24380.5105-0.8315-0.1770.00970.01410.99520.08010.11691.56620.5444-0.18370.5151-0.11770.75426.1963-14.1243-58.9914
152.7272-0.3891-1.34651.76851.01261.05730.0840.0461-0.8878-0.0214-0.2764-0.51050.94320.57830.10881.49720.6638-0.12930.20990.17940.594327.8388-13.4232-48.7171
166.1541-0.14613.61528.0321.3937.05510.12661.0109-0.2712-0.89390.2745-0.38110.13870.7931-0.30840.5258-0.0630.11140.3442-0.01060.32620.733744.2494-41.3749
171.3254-0.02580.07611.686-0.82052.49370.0135-0.25080.2180.15520.0237-0.2341-0.06950.3317-0.04140.2005-0.1046-0.01080.3077-0.08730.301422.487141.7983-20.9635
185.1141.35240.77252.643-1.25641.07790.0469-0.68770.62310.38280.10650.2253-0.35630.0265-0.19070.3008-0.1344-0.01120.3853-0.07850.293416.958943.4203-13.2185
192.1526-0.0086-0.02732.1696-0.04110.83910.0158-0.23750.02810.180.2552-0.3059-0.20470.4006-0.29850.183-0.0675-0.03150.3395-0.04430.256722.091739.0874-17.6142
203.262-0.98732.48361.08330.21062.93610.1378-0.2788-0.12390.3010.0372-0.38180.29880.174-0.18040.2094-0.063-0.04380.45840.04370.213727.941124.4936-12.3516
215.69791.5611-1.45373.64130.95134.29380.0795-0.3263-0.210.3817-0.11591.22490.5617-0.32350.00720.2613-0.11520.03020.35060.03330.36061.282113.9312-27.8046
222.24481.32330.58492.67870.61022.0450.0609-0.16240.16810.0379-0.06220.03190.26180.0424-0.00480.2031-0.0303-0.01530.24890.02870.198618.481817.569-30.1907
231.0430.87881.50071.69650.4824.6514-0.00990.01140.09610.0564-0.0898-0.2145-0.10280.34120.11870.1241-0.0579-0.00970.2438-0.02950.237819.062429.4222-23.6898
245.092.2868-1.59933.8871-1.605260.1976-0.9331-0.39010.7444-0.30180.24080.6261-0.1740.08270.3448-0.0953-0.01670.4744-0.00550.28537.244217.3672-20.417
256.7320.23430.44947.026-2.53972.516-0.08320.1207-0.87560.3546-0.258-0.55860.89230.26850.29470.4760.0871-0.10650.52870.03790.379834.631712.0097-7.3073
265.5872-4.48390.04163.88480.36020.5759-0.1528-0.067-1.5656-0.3932-0.07470.97231.0197-0.8093-0.11390.8663-0.2532-0.04420.74430.08940.918322.577313.7081-10.4423
275.76692.282-1.53278.7667-0.05223.1599-0.3842-1.1054-0.55321.40340.28780.05570.1051-0.00920.04880.36970.030.02970.5099-0.00920.200828.717221.291-3.2587
282.57850.05090.37422.78290.54562.94740.03640.07110.19120.0235-0.0526-0.0286-0.56710.1388-0.03650.5165-0.12240.04580.15850.00560.336910.423562.0679-50.5994
290.9022-0.2732-0.04390.6386-0.21920.46510.0681-0.51830.2378-0.01590.0026-0.0453-1.09050.0440.01520.903-0.22920.07130.0164-0.1630.350912.5467.1236-36.3377
304.60010.6337-0.65654.0504-2.60743.60690.0533-0.2455-0.53420.1780.71760.9290.0381-0.7793-0.5050.1786-0.05350.08050.29420.0760.505-5.160141.7796-26.7127
310.5763-0.0637-0.23090.3141-0.46710.82910.1079-0.16840.06830.1058-0.0262-0.111-0.34030.1434-0.07960.3094-0.10380.03520.2061-0.03510.2711.167349.6937-31.9077
327.2962-1.034-4.92225.7723-0.78423.80180.305-0.64430.58480.43530.28630.5552-0.7291-0.093-0.56920.25560.00170.04080.26870.0230.374-2.521751.1221-26.9631
332.0429-1.26380.33628.1799-1.35467.7569-0.1405-0.1573-0.0080.25690.7529-0.4307-0.29231.4282-0.45350.5941-0.18510.02290.6705-0.35830.378421.227666.3254-18.8153
346.82671.63994.05173.95071.43727.78530.2253-1.59520.17710.7892-0.233-0.2344-0.9194-0.65680.04730.9102-0.11670.0690.6663-0.07630.452813.846869.0473-13.953
355.6560.8476-1.51030.5626-1.02172.0456-0.4925-1.08660.82580.965-0.19640.5574-0.27-0.43490.30331.07780.0397-0.0050.3862-0.18840.470111.616275.225-22.9986
369.14192.894-2.87488.4756-2.48712.02870.0779-0.9022-0.29341.0336-0.4732-0.40970.15220.63390.50310.3706-0.012-0.04020.33620.00540.36319.150731.4201-65.6249
371.92910.03930.25931.92660.01081.87150.09590.1740.2417-0.22340.01190.031-0.28990.0346-0.08410.26940.00920.0510.11640.04660.23847.518445.0009-81.7555
380.87790.81130.29281.8298-0.4710.6850.0046-0.06710.491-0.27830.10980.0567-0.97150.0677-0.2310.6832-0.10790.10660.07050.06710.47036.21263.4814-76.5012
397.2681-0.5145-0.49317.81964.66123.20960.0943-0.232-0.22720.0802-0.51930.6837-0.4222-1.20290.41470.3950.03530.08140.43490.06960.2791-12.176250.1578-52.943
400.29750.0514-0.06140.01120.14671.40820.1131-0.00970.14710.07540.04050.0574-0.41530.0675-0.12920.3318-0.01420.080.12970.03390.28334.80453.61-60.6103
412.4671-2.34230.4334.89430.79477.4651-0.0086-0.23450.6736-0.17230.02590.1333-1.1103-1.3746-0.05110.40920.09810.06120.4230.05380.3965-9.587454.4546-61.8823
422.65050.6141-0.26864.25981.27363.0986-0.05820.09141.3282-0.56820.16881.1942-1.3556-0.4694-0.19511.12160.0820.11920.37230.10530.75273.760974.9635-73.5194
433.8079-0.5184-1.08753.96350.58924.22-0.20310.6691.1553-0.66440.00190.3209-1.0682-0.1197-0.1170.83440.03490.1391-0.09210.44890.6921.417670.1058-81.5839
447.3707-2.76792.61358.3915-1.62625.3118-0.2501-0.8847-1.99510.35050.60111.02290.4246-0.6973-0.29620.4845-0.0990.11790.46690.08950.4564-48.609833.3716-38.4966
452.8049-0.44460.63372.0660.61263.15810.02050.18970.3963-0.373-0.01210.3009-0.515-0.3562-0.0420.33160.16920.01070.32480.07120.3079-50.159950.3149-55.543
460.66340.26210.06581.68670.03990.57870.00780.5170.175-0.2382-0.01110.3683-0.4065-0.64270.03170.35960.1682-0.02720.6250.15460.3248-52.598944.2818-66.4647
471.0709-0.8302-0.75412.75060.53961.92260.03450.1904-0.0093-0.18330.0436-0.0681-0.074-0.3205-0.09510.1532-0.05270.01310.26360.0380.1568-38.584329.2861-65.1
483.6818-0.6241-4.44424.56042.66857.00790.21680.59910.3544-0.71540.1552-0.5098-0.5717-0.1623-0.32980.2757-0.00170.0830.30170.14120.3397-31.214335.288-70.9893
492.9052-0.5437-1.92715.1651-1.77992.9016-0.15861.357-0.3257-1.6764-0.18240.4660.4343-0.77520.17350.73570.1209-0.1311.4230.00170.4352-57.573635.5476-87.2032
507.74863.24213.5879.10693.8047.4126-0.09752.11-0.6175-0.60140.1361-1.2559-0.5948-0.1568-0.20950.62430.02280.01741.0464-0.02310.5167-47.342637.5758-83.3027
511.57341.1462-0.06793.2280.90940.3866-0.35270.71420.4558-1.26430.22270.3591-0.8281-0.12590.27710.76180.2464-0.07061.18290.33810.2151-54.367246.3127-81.8453
522.8490.13370.19463.61530.43161.47430.09840.08150.0188-0.15170.03530.1420.0883-0.3813-0.08380.2407-0.1329-0.06750.36440.06370.1944-46.266616.4858-69.1765
530.59880.0260.51540.6839-0.02640.51110.0002-0.0093-0.2469-0.27740.14370.09340.3488-0.1079-0.11370.4842-0.2396-0.07710.3618-0.02030.2555-44.21861.7429-71.9821
545.85920.5625-0.45717.7413-4.10735.66480.02170.210.0618-0.6342-0.5752-0.97810.49321.16690.51470.2937-0.05270.07850.44820.04660.3209-16.17744.3026-55.7335
551.1724-0.16730.24650.5269-0.40810.86260.0602-0.04-0.233-0.1023-0.00080.1270.4129-0.2003-0.06390.318-0.1273-0.02540.2368-0.00380.2125-34.89271.7516-56.5933
568.4719-4.5742-0.725.0624-1.02568.21380.36330.5909-0.5899-0.4707-0.618-0.06240.95980.77930.10960.333-0.0658-0.05410.4278-0.01160.2165-22.23691.3133-63.468
575.4593-0.99-0.88536.45590.58773.95460.4052-0.1088-1.64410.3965-0.3160.2891.5530.12210.10691.1342-0.1737-0.24650.4222-0.0370.6925-42.5201-21.1085-70.2027
583.322-0.3956-1.88568.2428-2.79492.18850.0493-0.3386-0.61790.9924-0.5027-1.0060.02861.03770.12070.9901-0.0395-0.43110.6347-0.08870.7929-33.1244-13.0487-70.435
594.4831-0.33691.51521.562-1.07771.6980.17950.6804-0.8355-0.90010.3794-0.45750.53450.2903-0.44070.7086-0.2413-0.0650.3686-0.14250.354-41.1355-12.1396-78.9019
604.60180.3389-0.12442.1530.54336.92720.26810.03520.34530.4388-0.12680.7729-0.4327-0.6367-0.15560.2969-0.0514-0.00640.5030.01130.3373-44.79618.2789-48.2787
612.5693-0.3064-0.25781.471-0.10550.8696-0.1927-0.2418-0.5615-0.04450.19460.13070.6587-0.2521-0.00020.457-0.18780.00880.24250.06090.2872-37.1703-10.6162-44.3771
623.52030.97540.85232.7483-1.45061.374-0.06360.5279-0.9014-0.5594-0.0021-0.19521.00740.0620.18370.6325-0.10780.01370.15420.00170.3769-30.1149-16.1026-47.9908
631.15770.01740.21551.1848-0.15080.3724-0.0933-0.3434-0.5162-0.00670.02740.10570.6259-0.1285-0.01410.6309-0.0730.0850.30990.14150.4166-33.102-15.3169-33.6267
645.27731.83940.02414.63252.96317.1729-0.0665-0.2859-0.069-0.0860.7397-0.75840.01081.7441-0.36520.23690.01120.00010.5462-0.11560.3407-11.88598.6473-28.0166
651.510.1103-0.00571.39211.3381.4032-0.0913-0.1836-0.19880.1210.04330.04230.27490.0450.06420.2254-0.0245-0.00110.2580.07680.1817-29.25681.2635-27.5021
667.7582-1.54484.46466.49531.44723.4670.1684-0.6424-0.75870.49270.3532-0.64540.74110.5281-0.44040.28440.04030.01310.5120.06720.3659-15.1005-1.1197-28.3804
674.59862.2825-1.78645.8311-2.55213.21680.2329-0.9647-0.2380.76050.17630.49370.8475-0.7021-0.35730.96170.09170.0570.87810.33410.5929-35.1476-18.3166-12.6033
684.03321.2287-2.19116.0425-4.37479.3466-0.0025-0.9448-0.50610.2020.48210.79140.65840.4229-0.52860.9661-0.0442-0.08730.69260.19050.635-25.05-20.756-15.2874
694.38463.8879-0.90343.7891-1.08140.43010.2708-0.6519-1.0280.759-0.3238-0.29061.35340.5424-0.03981.06990.1390.10740.41510.2520.6063-27.6883-25.2386-22.8061
702.19430.6314-0.77863.20960.30993.72130.06530.0596-0.0339-0.008-0.06510.12530.29410.1325-0.04380.2498-0.02610.00630.29710.10490.1766-33.55516.3771-14.7681
710.84820.3565-0.3291.7774-0.2881.68920.0816-0.21530.01970.4636-0.08080.21840.01740.0766-0.020.2846-0.07060.03870.35060.03020.1717-34.24116.6376-3.5994
723.34451.37170.14784.8693-0.50162.3801-0.21910.090.2893-0.1241-0.2005-1.2873-0.16510.76850.2060.2082-0.10120.06650.40710.12810.5853-17.126336.1413-22.7277
730.59940.12090.0572.4207-0.39530.80060.0609-0.13280.09810.0752-0.09450.0808-0.07570.02110.02350.1441-0.04740.01430.27860.0460.1708-33.398928.6757-17.0298
745.61483.57432.14093.85990.9230.93770.2611-0.73630.51160.5258-0.7384-0.3392-0.12140.34670.40770.232-0.1587-0.07410.50820.14410.359-19.669631.6587-14.096
759.48341.69331.54098.2994-1.66431.84790.1993-0.54581.07561.01250.30010.9121-1.2465-0.1345-0.48541.0661-0.16940.21390.484-0.06450.3983-42.548132.83395.6425
761.90231.35110.61452.17930.10840.2920.3077-0.59020.76871.1709-0.40730.4342-0.7755-0.0012-0.05571.9816-0.57560.13070.5319-0.17830.6121-33.890435.69358.5322
770.48130.1394-0.70751.9982-1.00271.34720.3835-0.46980.41191.4964-0.37980.0089-0.6070.3298-0.02511.0211-0.46530.09170.48280.16060.1136-31.958824.9139.5415
786.0351-0.94381.86597.3664-0.88532.09160.33310.743-0.9017-0.6077-0.33640.2280.8222-0.5110.0970.3195-0.1004-0.06420.4094-0.02190.2292-43.894723.2268-25.4429
792.936-0.01750.23493.4835-0.67132.55260.0548-0.15940.16830.2423-0.0696-0.1574-0.2735-0.01480.00250.2178-0.03210.06620.2626-0.01840.1536-41.243845.1464-15.8596
801.2141-0.3593-0.01420.5127-0.58341.22270.1188-0.10630.12390.04410.0269-0.0884-0.3472-0.0822-0.10950.2721-0.05630.07880.3242-0.01570.2247-43.518646.7769-18.7596
813.6524-2.2982-0.2422.99420.44971.75410.3760.00420.1733-0.0853-0.1920.1739-0.6122-0.5913-0.24310.35240.02110.08590.21620.03380.2269-49.51558.7496-28.4827
824.7660.93490.16154.739-1.96058.15160.09310.17450.25690.0457-0.1873-0.3904-0.82790.89760.11330.3098-0.07580.12160.3441-0.01740.2965-24.811348.9324-47.3114
830.79570.3381-0.40580.2815-0.02382.82520.16040.03620.1723-0.08290.00510.0323-0.2188-0.2375-0.13470.21690.01990.05980.20540.03170.2179-41.791345.956-39.7265
845.77623.7411-2.54655.4759-4.02338.70570.19130.01481.13940.02720.08050.0271-1.17880.1697-0.26460.4001-0.07930.07960.2306-0.02580.3077-29.995254.0657-40.3597
851.89440.4962-0.86142.24311.07049.34920.24130.97110.515-0.6789-0.14030.4276-0.9686-1.0343-0.07440.76720.27190.1390.55710.05040.5388-58.876264.1822-36.5885
862.54130.3104-0.03552.93611.52743.66910.06370.82850.7513-1.2974-0.2061-0.0924-0.85580.25040.01841.08090.27610.25860.66390.17150.5181-51.262769.7885-36.6741
875.2556-1.60430.87312.83580.30012.10070.0339-0.03241.11850.20380.1553-0.5782-1.3331-0.1396-0.16370.730.0480.1920.33790.01490.3833-49.709468.2795-26.8596
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 248 )
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 281 )
8X-RAY DIFFRACTION8chain 'A' and (resid 282 through 318 )
9X-RAY DIFFRACTION9chain 'A' and (resid 319 through 356 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 18 )
11X-RAY DIFFRACTION11chain 'B' and (resid 19 through 135 )
12X-RAY DIFFRACTION12chain 'B' and (resid 136 through 206 )
13X-RAY DIFFRACTION13chain 'B' and (resid 207 through 248 )
14X-RAY DIFFRACTION14chain 'B' and (resid 249 through 339 )
15X-RAY DIFFRACTION15chain 'B' and (resid 340 through 353 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 18 )
17X-RAY DIFFRACTION17chain 'C' and (resid 19 through 52 )
18X-RAY DIFFRACTION18chain 'C' and (resid 53 through 79 )
19X-RAY DIFFRACTION19chain 'C' and (resid 80 through 106 )
20X-RAY DIFFRACTION20chain 'C' and (resid 107 through 135 )
21X-RAY DIFFRACTION21chain 'C' and (resid 136 through 155 )
22X-RAY DIFFRACTION22chain 'C' and (resid 156 through 206 )
23X-RAY DIFFRACTION23chain 'C' and (resid 207 through 228 )
24X-RAY DIFFRACTION24chain 'C' and (resid 229 through 248 )
25X-RAY DIFFRACTION25chain 'C' and (resid 249 through 276 )
26X-RAY DIFFRACTION26chain 'C' and (resid 277 through 339 )
27X-RAY DIFFRACTION27chain 'C' and (resid 340 through 356 )
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 79 )
29X-RAY DIFFRACTION29chain 'D' and (resid 80 through 135 )
30X-RAY DIFFRACTION30chain 'D' and (resid 136 through 155 )
31X-RAY DIFFRACTION31chain 'D' and (resid 156 through 228 )
32X-RAY DIFFRACTION32chain 'D' and (resid 229 through 247 )
33X-RAY DIFFRACTION33chain 'D' and (resid 248 through 261 )
34X-RAY DIFFRACTION34chain 'D' and (resid 262 through 339 )
35X-RAY DIFFRACTION35chain 'D' and (resid 340 through 356 )
36X-RAY DIFFRACTION36chain 'E' and (resid 1 through 18 )
37X-RAY DIFFRACTION37chain 'E' and (resid 19 through 106 )
38X-RAY DIFFRACTION38chain 'E' and (resid 107 through 135 )
39X-RAY DIFFRACTION39chain 'E' and (resid 136 through 155 )
40X-RAY DIFFRACTION40chain 'E' and (resid 156 through 228 )
41X-RAY DIFFRACTION41chain 'E' and (resid 229 through 248 )
42X-RAY DIFFRACTION42chain 'E' and (resid 249 through 339 )
43X-RAY DIFFRACTION43chain 'E' and (resid 340 through 356 )
44X-RAY DIFFRACTION44chain 'F' and (resid 1 through 18 )
45X-RAY DIFFRACTION45chain 'F' and (resid 19 through 79 )
46X-RAY DIFFRACTION46chain 'F' and (resid 80 through 135 )
47X-RAY DIFFRACTION47chain 'F' and (resid 136 through 228 )
48X-RAY DIFFRACTION48chain 'F' and (resid 229 through 248 )
49X-RAY DIFFRACTION49chain 'F' and (resid 249 through 275 )
50X-RAY DIFFRACTION50chain 'F' and (resid 276 through 339 )
51X-RAY DIFFRACTION51chain 'F' and (resid 340 through 356 )
52X-RAY DIFFRACTION52chain 'G' and (resid 1 through 79 )
53X-RAY DIFFRACTION53chain 'G' and (resid 80 through 135 )
54X-RAY DIFFRACTION54chain 'G' and (resid 136 through 155 )
55X-RAY DIFFRACTION55chain 'G' and (resid 156 through 228 )
56X-RAY DIFFRACTION56chain 'G' and (resid 229 through 248 )
57X-RAY DIFFRACTION57chain 'G' and (resid 249 through 275 )
58X-RAY DIFFRACTION58chain 'G' and (resid 276 through 339 )
59X-RAY DIFFRACTION59chain 'G' and (resid 340 through 356 )
60X-RAY DIFFRACTION60chain 'H' and (resid 1 through 18 )
61X-RAY DIFFRACTION61chain 'H' and (resid 19 through 52 )
62X-RAY DIFFRACTION62chain 'H' and (resid 53 through 79 )
63X-RAY DIFFRACTION63chain 'H' and (resid 80 through 135 )
64X-RAY DIFFRACTION64chain 'H' and (resid 136 through 155 )
65X-RAY DIFFRACTION65chain 'H' and (resid 156 through 228 )
66X-RAY DIFFRACTION66chain 'H' and (resid 229 through 248 )
67X-RAY DIFFRACTION67chain 'H' and (resid 249 through 263 )
68X-RAY DIFFRACTION68chain 'H' and (resid 264 through 339 )
69X-RAY DIFFRACTION69chain 'H' and (resid 340 through 356 )
70X-RAY DIFFRACTION70chain 'I' and (resid 1 through 79 )
71X-RAY DIFFRACTION71chain 'I' and (resid 80 through 135 )
72X-RAY DIFFRACTION72chain 'I' and (resid 136 through 155 )
73X-RAY DIFFRACTION73chain 'I' and (resid 156 through 228 )
74X-RAY DIFFRACTION74chain 'I' and (resid 229 through 248 )
75X-RAY DIFFRACTION75chain 'I' and (resid 249 through 261 )
76X-RAY DIFFRACTION76chain 'I' and (resid 262 through 339 )
77X-RAY DIFFRACTION77chain 'I' and (resid 340 through 356 )
78X-RAY DIFFRACTION78chain 'J' and (resid 1 through 18 )
79X-RAY DIFFRACTION79chain 'J' and (resid 19 through 79 )
80X-RAY DIFFRACTION80chain 'J' and (resid 80 through 106 )
81X-RAY DIFFRACTION81chain 'J' and (resid 107 through 135 )
82X-RAY DIFFRACTION82chain 'J' and (resid 136 through 155 )
83X-RAY DIFFRACTION83chain 'J' and (resid 156 through 228 )
84X-RAY DIFFRACTION84chain 'J' and (resid 229 through 248 )
85X-RAY DIFFRACTION85chain 'J' and (resid 249 through 262 )
86X-RAY DIFFRACTION86chain 'J' and (resid 263 through 339 )
87X-RAY DIFFRACTION87chain 'J' and (resid 340 through 356 )

+
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

-
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