- PDB-4ac5: Lipidic sponge phase crystal structure of the Bl. viridis reactio... -
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基本情報
登録情報
データベース: PDB / ID: 4ac5
タイトル
Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography
要素
(REACTION CENTER PROTEIN ...) x 3
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
キーワード
PHOTOSYNTHESIS / LIPIDIC-SPONGE PHASE / REACTION CENTER / ELECTRON TRANSPORT / CELL MEMBRANE / METAL- BINDING / TRANSMEMBRANE / FORMYLATION / CHROMOPHORE / LIPOPROTEIN
機能・相同性
機能・相同性情報
plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding 類似検索 - 分子機能
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile. 類似検索 - ドメイン・相同性
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit 類似検索 - 構成要素
C: PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT H: REACTION CENTER PROTEIN H CHAIN L: REACTION CENTER PROTEIN L CHAIN M: REACTION CENTER PROTEIN M CHAIN ヘテロ分子
マシュー密度: 3.4 Å3/Da / 溶媒含有率: 64 % 解説: THE DATA WERE COLLECTED AT THE LINAC COHERENT LIGHT SOURCE USING SERIAL FEMTOSECOND CRYSTALLOGRAPHY TO PROVE THAT THE SPONGE PHASE CRYSTALLISATION METHOD IS COMPATABLE WITH SERIAL FEMTOSECOND ...解説: THE DATA WERE COLLECTED AT THE LINAC COHERENT LIGHT SOURCE USING SERIAL FEMTOSECOND CRYSTALLOGRAPHY TO PROVE THAT THE SPONGE PHASE CRYSTALLISATION METHOD IS COMPATABLE WITH SERIAL FEMTOSECOND CRYSTALLOGRAPHY. THE DATA WAS MERGED FROM 265 MICROCRYSTALS USING THE IN-HOUSE PROGRAM CRYSTFEL 0.1.0 AND INDEXAMAJIG.
結晶化
pH: 7.9 詳細: BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (20-30 MG/ML) , 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M- 600, 1.0 M HEPES PH ...詳細: BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (20-30 MG/ML) , 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M- 600, 1.0 M HEPES PH 8.0, 0.7 M (NH4)2SO4, 2.5 % 1,2,3- HEPTANETRIOL) AND 50 UL 1.0-1.2 M TRI-SODIUM CITRATE
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データ収集
回折
平均測定温度: 288 K / Serial crystal experiment: Y
放射光源
由来: 自由電子レーザー / サイト: SLAC LCLS / ビームライン: AMO / 波長: 6.2 / 波長: 6.2 Å
解像度: 8.2→46.1 Å / Cor.coef. Fo:Fc: 0.665 / SU ML: 9.332 / 交差検証法: THROUGHOUT / ESU R Free: 7.361 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
Rfactor
反射数
%反射
Selection details
Rfree
0.384
95
4.8 %
RANDOM
Rwork
0.35071
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obs
0.35239
1899
96.94 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK