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- PDB-6b55: Crystal structure of the Plant Defensin NaD1 complexed with phosp... -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6b55
タイトルCrystal structure of the Plant Defensin NaD1 complexed with phosphatidic acid
要素Flower-specific defensin
キーワードANTIMICROBIAL PROTEIN / antimicrobial / antifungal / defensin / PLANT PROTEIN
機能・相同性
機能・相同性情報


vacuole / defense response to fungus / killing of cells of another organism / extracellular region
類似検索 - 分子機能
Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE / TRIETHYLENE GLYCOL / PHOSPHATE ION / Flower-specific defensin
類似検索 - 構成要素
生物種Nicotiana alata (ヤバネタバコ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å
データ登録者Jarva, M. / Phan, K. / Humble, C. / Lay, F.T. / Hulett, M. / Kvansakul, M.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC)FT130101349 オーストラリア
引用ジャーナル: Nat Commun / 年: 2018
タイトル: X-ray structure of a carpet-like antimicrobial defensin-phospholipid membrane disruption complex.
著者: Jarva, M. / Lay, F.T. / Phan, T.K. / Humble, C. / Poon, I.K.H. / Bleackley, M.R. / Anderson, M.A. / Hulett, M.D. / Kvansakul, M.
履歴
登録2017年9月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年5月23日Provider: repository / タイプ: Initial release
改定 1.12018年5月30日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22018年8月15日Group: Data collection / Database references / カテゴリ: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
改定 1.32019年2月20日Group: Author supporting evidence / Data collection / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年10月4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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.62024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Flower-specific defensin
B: Flower-specific defensin
C: Flower-specific defensin
D: Flower-specific defensin
E: Flower-specific defensin
F: Flower-specific defensin
G: Flower-specific defensin
H: Flower-specific defensin
I: Flower-specific defensin
J: Flower-specific defensin
K: Flower-specific defensin
L: Flower-specific defensin
M: Flower-specific defensin
N: Flower-specific defensin
O: Flower-specific defensin
P: Flower-specific defensin
Q: Flower-specific defensin
R: Flower-specific defensin
S: Flower-specific defensin
T: Flower-specific defensin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)115,00447
ポリマ－107,72920
非ポリマー7,27527
水8,125451
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: assay for oligomerization, BS3 Crosslinking assay visualized lipid mediated oligomerization on SDS-PAGE
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)114.218, 154.925, 135.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDモデル要素
11G-215-

HOH

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要素

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タンパク質・ペプチド , 1種, 20分子 ABCDEFGHIJKLMNOPQRST

#1: タンパク質・ペプチド
Flower-specific defensin


分子量: 5386.455 Da / 分子数: 20 / 由来タイプ: 組換発現 / 由来: (組換発現) Nicotiana alata (ヤバネタバコ) / 発現宿主: Komagataella pastoris (菌類) / 参照: UniProt: Q8GTM0

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非ポリマー , 5種, 478分子

#2: 化合物
ChemComp-PA8 / 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE


分子量: 423.458 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C19H36O8P / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 3 / 由来タイプ: 合成 / 式: PO4
#4: 化合物
ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C6H14O4
#5: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C2H6O2
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 451 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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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: 2.79 Å3/Da / 溶媒含有率: 55.95 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.89
詳細: 28% PEG 4000, 1M sodium chloride, 0.1M trisodium-citrate-citric acid, pH 5.89

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2016年7月20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: 0.9537 Å / 相対比: 1
反射解像度: 2.5→47.06 Å / Num. obs: 41102 / % possible obs: 98.4 % / 冗長度: 2.9 % / Biso Wilson estimate: 33.58 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.082 / Rrim(I) all: 0.146 / Net I/σ(I): 7.6
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.62.90.7147170.630.4920.86899.8
9.01-47.0630.0288500.9990.0190.03490.3

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
Aimless0.5.32データ削減
PHASER2.7.16位相決定
PHENIX1.12精密化
PDB_EXTRACTデータ抽出
Coot0.8.8モデル構築
XDS20161205data processing
XDS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: 4AAZ

4aaz


解像度: 2.5→44.469 Å / SU ML: 0.35 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.4
Rfactor反射数%反射
Rfree0.2519 2042 4.97 %
Rwork0.2031 --
obs0.2056 41062 97.72 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 108.8 Å2 / Biso mean: 43.3408 Å2 / Biso min: 12.32 Å2
精密化ステップサイクル: final / 解像度: 2.5→44.469 Å
タンパク質核酸リガンド溶媒全体
原子数7380 0 475 451 8306
Biso mean--64.2 36.44 -
残基数----960
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0038028
X-RAY DIFFRACTIONf_angle_d0.71210714
X-RAY DIFFRACTIONf_chiral_restr0.0481154
X-RAY DIFFRACTIONf_plane_restr0.0061308
X-RAY DIFFRACTIONf_dihedral_angle_d13.0935436
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.55820.36441380.309526072745100
2.5582-2.62220.38621360.295526332769100
2.6222-2.6930.34011300.27662634276499
2.693-2.77230.34031460.26492619276599
2.7723-2.86170.28591290.25472611274099
2.8617-2.9640.30731310.24392615274699
2.964-3.08260.3171450.26262626277199
3.0826-3.22290.2951230.23282647277099
3.2229-3.39280.2581300.20982597272798
3.3928-3.60520.23831480.18582595274398
3.6052-3.88350.2521520.17252599275198
3.8835-4.2740.2061200.162581270197
4.274-4.89180.17441380.14062575271396
4.8918-6.16050.18441360.17362556269294
6.1605-44.4760.22391400.18372525266590
精密化 TLS

手法: refined / 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)
10.12450.0483-0.09270.0423-0.10.12010.07730.0154-0.0005-0.4907-0.2798-0.06710.54520.2893-0.00030.4442-0.0323-0.04640.3882-0.0370.3211-4.6255126.0458-0.7788
20.0560.0624-0.06290.10740.14730.16580.0399-0.1257-0.2283-0.0701-0.0474-0.15920.18320.086-0.00020.1794-0.0078-0.02140.2606-0.01150.24830.7286116.09239.1198
30.27330.1974-0.23560.45370.33940.50460.0092-0.18990.74670.01190.03940.18160.00590.130800.26830.01810.01530.2620.00350.2757-0.5429121.60153.8653
40.0710.0629-0.19980.5013-0.10270.2571-0.2310.07980.26290.06140.0916-0.66790.09610.1398-0.00010.39980.01330.00460.30330.03740.5397-3.947138.8354-4.2715
51.00150.40170.15690.3491-0.02011.8756-0.1296-0.1480.6510.0270.1667-0.5209-0.1855-0.1211-0.00490.21980.0075-0.01410.16890.02260.5415-2.618136.5037-1.9847
60.44640.2671-0.13640.1782-0.0120.1194-0.0637-0.1625-0.0549-0.2526-0.1532-0.17280.16820.2912-0.00310.32760.11580.06140.3375-0.00790.33148.1255110.2236-11.3039
70.00120.05620.05550.13130.17720.26940.29440.0038-0.71280.29690.05530.14470.47490.09360.0090.32490.001-0.04630.31570.04840.347611.4579101.51310.4223
80.48960.11790.48310.08760.29091.28510.37740.1876-0.7240.06960.16280.0150.16680.65970.12340.35580.0480.05540.2892-0.01820.31888.9892102.688-6.2776
90.0318-0.0379-0.06650.15010.0090.1487-0.01620.23280.22660.1131-0.25870.1240.33920.4209-0.00990.24420.0453-0.00080.2174-0.03560.26412.1528109.4381-3.9605
101.8546-1.6393-1.73621.4411.52081.6176-0.52340.7527-0.47840.22810.19020.47920.3974-0.3239-0.51880.26070.04120.0210.43650.2140.25813.7046113.3461-8.908
110.51970.18580.06210.54740.62780.6309-0.46450.34920.6306-0.37510.3640.0106-0.6080.41610.00490.2650.0023-0.03730.33010.07710.29184.846126.1786-16.9032
120.1296-0.0288-0.02250.1458-0.08110.03860.0271-0.24390.1052-0.3763-0.2853-0.0447-0.29940.11640.00030.2875-0.0010.02130.37430.01440.22311.6272119.9811-14.9341
130.3478-0.2583-0.04150.20640.2690.55180.170.00180.2437-0.1965-0.34630.09780.2215-0.1904-0.05910.29150.0032-0.04460.31430.08510.25997.4511121.1138-9.9183
140.22330.4814-0.11181.2065-0.35190.0692-0.0426-0.4610.14420.0822-0.008-0.93080.23010.06790.06860.2711-0.12310.17660.39190.02820.345929.9077104.2298-12.3107
150.0691-0.098-0.12090.25440.03010.1847-0.1317-0.0112-0.09230.18350.0213-0.05470.26270.08050.00010.39450.07830.02370.32840.03670.412230.417494.8547-0.3653
160.2012-0.0812-0.08350.09280.24670.46880.1326-0.2601-0.3506-0.01670.3595-0.21680.30040.49420.01210.2730.0444-0.00130.30330.02290.374630.2442100.8129-5.2683
170.1861-0.20040.10483.348-0.06150.07570.03030.2304-0.0865-0.31970.93170.3469-0.5144-0.93410.31410.371-0.019-0.0280.48340.05270.272224.2233104.392-13.0468
181.10160.20170.69580.760.8331.00890.45970.1023-0.1448-0.1748-0.1307-0.1534-0.1721-0.03650.33030.28930.0346-0.00960.31560.04390.196822.773115.8368-19.3875
192.1893-0.59310.12861.37540.043.21150.324-0.1798-0.185-0.52140.2847-0.24880.18420.30041.03920.24890.0012-0.00660.35540.01640.214323.9854112.8264-11.9808
200.23610.04740.0540.0644-0.05180.0488-0.3325-0.37030.6575-0.22440.0925-0.33390.15670.59070.00010.40810.0164-0.04270.40450.05780.3663-2.557164.9966-21.1493
210.19380.1490.02860.3154-0.22250.11420.422-0.0188-0.3884-0.10820.0435-0.32020.2798-0.09850.00110.3377-0.0296-0.04980.27990.0520.3004-4.2555153.4063-16.3811
220.7042-0.26320.65390.3289-0.19280.8972-0.4943-0.03990.0993-0.06370.20630.0624-0.5782-0.2802-0.02710.3178-0.0046-0.01590.2318-0.06750.24490.8649159.809-16.1472
231.21810.40450.78280.1470.18860.8551-0.5496-0.1769-0.05160.5270.28750.6541-0.01910.106-0.19430.48850.17260.07790.2964-0.01260.3583-4.9974168.7309-17.0765
240.19290.0096-0.18180.06030.12860.2304-0.11590.03170.07380.11150.1176-0.006-0.0682-0.042700.2250.0155-0.05170.23-0.01160.1852.8424181.3429-20.3403
250.186-0.2694-0.25390.29990.29430.3323-0.251-0.03840.0713-0.04850.1660.1903-0.10830.1437-0.00250.29260.013-0.0060.31120.01660.24840.3621174.7606-17.5582
260.0518-0.00890.03290.1261-0.09030.0321-0.2556-0.3373-0.4842-0.0563-0.14960.0590.07230.11080.00080.32250.03170.01670.35270.05150.389513.25151.4789-30.1817
270.2621-0.15210.07990.18580.18450.2825-0.0075-0.0044-0.3027-0.3469-0.04840.48260.1729-0.0079-0.00020.213-0.0217-0.02840.1635-0.01230.22099.5106139.9362-25.0591
280.6243-0.0497-0.44390.22170.09970.2719-0.2812-0.14120.1273-0.2955-0.0036-0.2877-0.16670.1303-0.11460.39390.0493-0.08850.2301-0.01690.267612.6225147.137-22.7804
290.31820.8147-0.40042.3175-0.63221.37160.34430.04630.2710.1280.68290.7748-0.3524-0.22290.57330.35160.0737-0.0020.46750.03740.41088.6789155.1811-28.5869
300.04660.1501-0.12690.282-0.32740.32490.30840.2994-0.02060.4426-0.27730.2976-0.32080.09070.02610.22420.0387-0.0050.1678-0.028-0.407814.3047168.3453-29.5423
310.1905-0.13240.15730.19540.08770.21680.1223-0.1652-0.35090.0057-0.16920.11840.4660.1334-0.00040.40710.0127-0.05640.264-0.00210.352511.5979161.3622-27.628
320.08880.11040.21210.5404-0.07490.75430.5261-0.35090.2771-0.6299-0.3599-0.81920.49470.04380.15020.54730.11420.18230.63140.03950.555331.6693144.1601-27.9246
330.17630.0042-0.01820.0061-0.01170.03950.26710.137-0.2873-0.3001-0.28730.03270.28470.7651-0.01480.32590.0419-0.10630.2442-0.04790.200522.1875132.878-20.2654
340.0811-0.02330.03480.10880.02010.0222-0.20410.0461-0.1838-1.0058-0.2710.5730.0274-0-0.00070.42060.04270.00020.33880.05760.31929.1624130.3094-24.6403
350.1581-0.087-0.12030.0961-0.05370.1386-0.35060.21660.337-0.0596-0.22580.35960.34970.13490.00010.33880.0473-0.03140.2890.02060.314429.6578135.5585-27.3772
361.7010.85531.63810.55970.9391.6703-0.0863-0.11060.2357-0.3699-0.60450.1315-0.308-0.6884-0.59390.39460.13380.04060.29060.08150.313627.7413140.429-21.4694
370.25050.00750.26030.5986-0.51270.75110.4099-0.35560.0537-0.7523-0.1930.30360.57370.506-0.00680.49440.15340.0840.54660.15840.698826.8797146.8867-29.6752
380.6361-1.28250.78712.6479-1.61520.98030.1588-0.0732-0.17080.8227-0.6469-0.8421-0.63380.4119-0.2180.27880.0255-0.08830.48430.12240.613232.7264161.6734-24.0166
391.31951.76790.20123.87521.37862.8440.15710.11910.3033-0.1161-0.8268-0.408-0.20050.6981-0.67740.36440.11940.05910.29140.14630.366229.2591161.0215-32.0673
400.4506-0.26870.30450.38740.34321.2691-0.1965-0.094-0.018-0.0873-0.3625-0.60090.61870.0249-0.22430.40740.0880.06440.33570.07050.368328.2779154.236-27.3018
410.0295-0.015-0.09120.01970.10670.2438-0.6998-0.5190.46910.84960.3051-0.4371-0.0320.1156-0.00980.4854-0.0106-0.11370.4944-0.00260.547844.9255135.849-11.2253
420.5674-0.5455-0.35410.61460.39340.5129-0.15270.1618-0.49330.0861-0.11550.215-0.1709-0.1192-0.08610.1721-0.01310.03030.15320.05480.186937.1602123.0049-8.9869
430.2033-0.23640.24220.3412-0.40040.4658-0.0342-0.11660.4745-0.0294-0.1435-0.1662-0.07290.0277-0.00120.20510.0160.00190.26520.01660.35939.7581130.1169-8.9761
440.1589-0.1108-0.27030.16510.09090.43570.2481-0.1581-0.3339-0.40930.22170.15450.2468-0.22550.03550.4781-0.0159-0.24160.34510.09890.7543.001137.311-16.5017
450.5199-0.6541-0.56270.82890.71850.58540.52530.10940.8423-0.4636-0.0786-0.4131-0.29360.02380.15810.25970.0651-0.02030.27550.07090.69342.6776152.9617-11.8593
460.1450.022-0.0351-0.0095-0.02320.0358-0.4217-0.47510.2636-0.84620.5090.1959-0.3828-0.3639-0.00010.48820.03910.03250.3640.16690.606445.4179151.0657-19.758
470.2286-0.0937-0.22930.10920.47552.0046-0.10360.10710.4722-0.2096-0.1369-0.70.3156-0.3154-0.06930.28570.03520.07510.23830.01090.478642.0322144.6827-15.6435
480.26340.1846-0.08080.1769-0.10460.111-0.39920.19880.20940.4092-0.1745-0.571-0.07990.5533-0.00650.4451-0.0182-0.09650.58420.09640.421315.8071196.9564-30.8593
490.28150.0816-0.16860.04970.04160.14360.11850.14660.1627-0.02390.1120.2275-0.04840.04120.0020.2794-0.0428-0.04390.38420.03330.211817.2821184.1641-32.7049
500.07660.1343-0.02250.2443-0.04420.0055-0.2568-0.07140.2623-0.22550.4407-0.43620.4397-0.55770.0971-0.1469-0.2145-0.11610.3320.03650.391915.8583185.874-20.2349
510.02380.02840.00780.07940.12390.14260.13470.12630.43620.0213-0.25360.0495-0.26580.10550.00050.5060.0520.01340.44860.08470.407516.2885193.4096-33.3994
520.0705-0.0736-0.0180.08660.08480.0177-0.3365-0.3192-0.37410.2620.1012-0.08090.11640.0169-00.525-0.0342-0.08990.43020.02530.469810.1516197.6052-30.4536
530.32020.3097-0.4631.96550.64691.6267-0.66410.23851.08180.8416-0.03240.1698-0.4997-0.258-0.32440.47650.1228-0.21440.45920.10350.60619.4697210.4497-22.9967
540.6660.13660.04850.23150.03450.0092-0.02130.05750.7733-0.0549-0.03260.6322-0.4135-0.3878-0.02090.4110.0562-0.12560.38730.12670.42019.4358202.9023-24.7453
552.01-0.82381.73180.3757-0.73151.5517-0.13680.39210.01450.7291-0.2279-0.6071-0.7365-0.4838-0.21730.4980.01490.01310.42760.02720.373836.3388190.2981-23.727
560.3211-0.1166-0.16150.13770.05250.8313-0.49020.3517-0.38610.3959-0.2802-0.33630.15340.4996-0.0570.3610.03580.00880.557-0.13140.294731.0017174.6814-26.5888
57-0.0005-0.0054-0.02750.0994-0.02510.0672-0.52640.2238-0.0490.02850.5070.110.28990.4358-0.0030.3887-0.01720.11370.5205-0.03120.369739.375176.3907-27.1812
580.0947-0.0716-0.04330.14970.14730.11230.1443-0.52970.13760.4126-0.0701-0.17390.80890.8008-00.35-0.05080.03570.3895-0.0080.326738.5213182.198-27.1533
590.0982-0.0133-0.0740.04760.00830.0569-0.5423-0.27340.35370.22470.44350.04780.5712-0.00410.00010.43540.01750.02040.3297-0.06670.2927.5606178.6964-17.9492
600.3628-0.0225-0.01580.03630.01720.0341-0.2620.68470.38240.17050.3034-0.10440.36820.09470.00020.3842-0.0221-0.00280.48490.05460.284437.6891186.7327-26.0362
610.64510.7596-0.50981.0572-0.36980.75480.1426-0.23010.448-0.2855-0.6050.5774-0.68720.012-0.03470.30980.0303-0.03140.54770.1980.342731.886192.4916-27.1313
621.19840.0442-0.3662-0.0006-0.05150.24370.14920.16721.4326-0.326-0.01860.0477-0.5536-0.01010.04510.4398-0.0386-0.08980.32680.14910.350529.176203.6216-20.9199
631.35340.10590.9030.575-0.00750.628-0.2324-0.59130.3415-0.0242-0.5123-0.2430.16420.121-1.31750.2335-0.00380.01030.15570.2917-0.108527.7162195.8469-20.4238
643.27840.09610.1782-0.01320.0306-0.0064-0.25370.1456-1.01660.94980.48530.34790.06780.25640.04250.71490.12010.05020.22780.03820.335644.68178.0422-7.1592
650.09420.12150.10090.10530.0730.051-0.05660.179-0.99060.10750.01830.2282-0.0887-0.1744-0.00030.6190.0510.08510.47150.00280.660540.5279164.4831-14.8828
660.0816-0.04510.050.0420.03310.13040.0169-0.0967-0.48620.24820.2378-0.0675-0.1555-0.32070.00010.40080.09670.03250.3434-0.00750.534247.4797166.9805-9.6881
670.2087-0.19890.03790.1671-0.06860.3296-0.7254-0.23420.21020.37830.63020.1369-0.0369-0.0090.00610.47110.08610.01740.33440.12910.668140.115171.8671-9.4404
680.21760.11490.16680.0130.10420.11130.46010.3445-0.4116-0.0432-0.0602-0.19270.7201-0.3942-0.00030.40120.0171-0.03760.4513-0.07110.333844.3703181.5231-12.0858
690.25970.17090.05480.11110.0235-0.0070.10290.2350.6830.2464-0.21690.2028-0.18540.2794-0.00480.2905-0.01870.06820.30470.01760.233636.3735192.649-3.1156
700.21480.3493-0.17670.8272-0.18430.3560.52060.02870.44840.7853-0.17420.3864-0.13580.05470.02590.26960.0702-0.00050.27920.03220.281642.088195.4038-8.8704
710.44840.445-0.17990.5687-0.34580.38340.01060.43370.842-0.33360.01860.3390.1846-0.09520.06140.2041-0.00130.02630.2065-0.04430.311544.212190.0714-9.5207
723.8271-0.006-0.8280.07570.08850.30230.0242-0.64870.005-0.3864-0.13960.10530.40940.322-0.07260.3390.011-0.0030.21780.01180.302537.9034185.5173-8.9304
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 6 )A0 - 6
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 26 )A7 - 26
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 47 )A27 - 47
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 26 )B0 - 26
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 47 )B27 - 47
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 6 )C0 - 6
7X-RAY DIFFRACTION7chain 'C' and (resid 7 through 26 )C7 - 26
8X-RAY DIFFRACTION8chain 'C' and (resid 27 through 34 )C27 - 34
9X-RAY DIFFRACTION9chain 'C' and (resid 35 through 47 )C35 - 47
10X-RAY DIFFRACTION10chain 'D' and (resid 0 through 6 )D0 - 6
11X-RAY DIFFRACTION11chain 'D' and (resid 7 through 26 )D7 - 26
12X-RAY DIFFRACTION12chain 'D' and (resid 27 through 34 )D27 - 34
13X-RAY DIFFRACTION13chain 'D' and (resid 35 through 47 )D35 - 47
14X-RAY DIFFRACTION14chain 'E' and (resid 0 through 6 )E0 - 6
15X-RAY DIFFRACTION15chain 'E' and (resid 7 through 26 )E7 - 26
16X-RAY DIFFRACTION16chain 'E' and (resid 27 through 47 )E27 - 47
17X-RAY DIFFRACTION17chain 'F' and (resid 0 through 6 )F0 - 6
18X-RAY DIFFRACTION18chain 'F' and (resid 7 through 34 )F7 - 34
19X-RAY DIFFRACTION19chain 'F' and (resid 35 through 47 )F35 - 47
20X-RAY DIFFRACTION20chain 'G' and (resid 0 through 6 )G0 - 6
21X-RAY DIFFRACTION21chain 'G' and (resid 7 through 34 )G7 - 34
22X-RAY DIFFRACTION22chain 'G' and (resid 35 through 47 )G35 - 47
23X-RAY DIFFRACTION23chain 'H' and (resid 0 through 6 )H0 - 6
24X-RAY DIFFRACTION24chain 'H' and (resid 7 through 26 )H7 - 26
25X-RAY DIFFRACTION25chain 'H' and (resid 27 through 47 )H27 - 47
26X-RAY DIFFRACTION26chain 'I' and (resid 0 through 6 )I0 - 6
27X-RAY DIFFRACTION27chain 'I' and (resid 7 through 34 )I7 - 34
28X-RAY DIFFRACTION28chain 'I' and (resid 35 through 47 )I35 - 47
29X-RAY DIFFRACTION29chain 'J' and (resid 0 through 6 )J0 - 6
30X-RAY DIFFRACTION30chain 'J' and (resid 7 through 26 )J7 - 26
31X-RAY DIFFRACTION31chain 'J' and (resid 27 through 47 )J27 - 47
32X-RAY DIFFRACTION32chain 'K' and (resid 0 through 6 )K0 - 6
33X-RAY DIFFRACTION33chain 'K' and (resid 7 through 16 )K7 - 16
34X-RAY DIFFRACTION34chain 'K' and (resid 17 through 26 )K17 - 26
35X-RAY DIFFRACTION35chain 'K' and (resid 27 through 34 )K27 - 34
36X-RAY DIFFRACTION36chain 'K' and (resid 35 through 47 )K35 - 47
37X-RAY DIFFRACTION37chain 'L' and (resid 0 through 6 )L0 - 6
38X-RAY DIFFRACTION38chain 'L' and (resid 7 through 16 )L7 - 16
39X-RAY DIFFRACTION39chain 'L' and (resid 17 through 26 )L17 - 26
40X-RAY DIFFRACTION40chain 'L' and (resid 27 through 47 )L27 - 47
41X-RAY DIFFRACTION41chain 'M' and (resid 0 through 6 )M0 - 6
42X-RAY DIFFRACTION42chain 'M' and (resid 7 through 26 )M7 - 26
43X-RAY DIFFRACTION43chain 'M' and (resid 27 through 47 )M27 - 47
44X-RAY DIFFRACTION44chain 'N' and (resid 0 through 6 )N0 - 6
45X-RAY DIFFRACTION45chain 'N' and (resid 7 through 16 )N7 - 16
46X-RAY DIFFRACTION46chain 'N' and (resid 17 through 26 )N17 - 26
47X-RAY DIFFRACTION47chain 'N' and (resid 27 through 47 )N27 - 47
48X-RAY DIFFRACTION48chain 'O' and (resid 0 through 6 )O0 - 6
49X-RAY DIFFRACTION49chain 'O' and (resid 7 through 34 )O7 - 34
50X-RAY DIFFRACTION50chain 'O' and (resid 35 through 40 )O35 - 40
51X-RAY DIFFRACTION51chain 'O' and (resid 41 through 47 )O41 - 47
52X-RAY DIFFRACTION52chain 'P' and (resid 0 through 6 )P0 - 6
53X-RAY DIFFRACTION53chain 'P' and (resid 7 through 27 )P7 - 27
54X-RAY DIFFRACTION54chain 'P' and (resid 28 through 47 )P28 - 47
55X-RAY DIFFRACTION55chain 'Q' and (resid 0 through 6 )Q0 - 6
56X-RAY DIFFRACTION56chain 'Q' and (resid 7 through 16 )Q7 - 16
57X-RAY DIFFRACTION57chain 'Q' and (resid 17 through 26 )Q17 - 26
58X-RAY DIFFRACTION58chain 'Q' and (resid 27 through 34 )Q27 - 34
59X-RAY DIFFRACTION59chain 'Q' and (resid 35 through 40 )Q35 - 40
60X-RAY DIFFRACTION60chain 'Q' and (resid 41 through 47 )Q41 - 47
61X-RAY DIFFRACTION61chain 'R' and (resid 0 through 6 )R0 - 6
62X-RAY DIFFRACTION62chain 'R' and (resid 7 through 34 )R7 - 34
63X-RAY DIFFRACTION63chain 'R' and (resid 35 through 47 )R35 - 47
64X-RAY DIFFRACTION64chain 'S' and (resid 0 through 6 )S0 - 6
65X-RAY DIFFRACTION65chain 'S' and (resid 7 through 16 )S7 - 16
66X-RAY DIFFRACTION66chain 'S' and (resid 17 through 34 )S17 - 34
67X-RAY DIFFRACTION67chain 'S' and (resid 35 through 47 )S35 - 47
68X-RAY DIFFRACTION68chain 'T' and (resid 0 through 6 )T0 - 6
69X-RAY DIFFRACTION69chain 'T' and (resid 7 through 16 )T7 - 16
70X-RAY DIFFRACTION70chain 'T' and (resid 17 through 26 )T17 - 26
71X-RAY DIFFRACTION71chain 'T' and (resid 27 through 34 )T27 - 34
72X-RAY DIFFRACTION72chain 'T' and (resid 35 through 47 )T35 - 47

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万見について

-
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://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