- PDB-4gqh: The Conformations and Interactions of the Four-Layer Aggregate Re... -
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基本情報
登録情報
データベース: PDB / ID: 4gqh
タイトル
The Conformations and Interactions of the Four-Layer Aggregate Revealed by X-ray Crystallography Diffraction Implied the Importance of Peptides at Opposite Ends in Their Assemblies
要素
Capsid protein
キーワード
VIRAL PROTEIN / Hydrogen-bonding / the Four-layer Aggregate
A: Capsid protein B: Capsid protein C: Capsid protein D: Capsid protein E: Capsid protein F: Capsid protein G: Capsid protein H: Capsid protein I: Capsid protein J: Capsid protein K: Capsid protein L: Capsid protein M: Capsid protein N: Capsid protein O: Capsid protein P: Capsid protein Q: Capsid protein R: Capsid protein S: Capsid protein T: Capsid protein U: Capsid protein V: Capsid protein W: Capsid protein X: Capsid protein Y: Capsid protein Z: Capsid protein a: Capsid protein b: Capsid protein c: Capsid protein d: Capsid protein e: Capsid protein f: Capsid protein h: Capsid protein i: Capsid protein
D: Capsid protein F: Capsid protein G: Capsid protein H: Capsid protein K: Capsid protein M: Capsid protein N: Capsid protein
A: Capsid protein B: Capsid protein C: Capsid protein E: Capsid protein I: Capsid protein J: Capsid protein L: Capsid protein O: Capsid protein P: Capsid protein Q: Capsid protein
D: Capsid protein F: Capsid protein G: Capsid protein H: Capsid protein K: Capsid protein M: Capsid protein N: Capsid protein
A: Capsid protein B: Capsid protein C: Capsid protein E: Capsid protein I: Capsid protein J: Capsid protein L: Capsid protein O: Capsid protein P: Capsid protein Q: Capsid protein
R: Capsid protein T: Capsid protein U: Capsid protein c: Capsid protein d: Capsid protein e: Capsid protein h: Capsid protein i: Capsid protein
S: Capsid protein V: Capsid protein W: Capsid protein X: Capsid protein Y: Capsid protein Z: Capsid protein a: Capsid protein b: Capsid protein f: Capsid protein
R: Capsid protein T: Capsid protein U: Capsid protein c: Capsid protein d: Capsid protein e: Capsid protein h: Capsid protein i: Capsid protein
S: Capsid protein V: Capsid protein W: Capsid protein X: Capsid protein Y: Capsid protein Z: Capsid protein a: Capsid protein b: Capsid protein f: Capsid protein
分子量: 19350.453 Da / 分子数: 34 / 断片: UNP residues 2-155 / 由来タイプ: 組換発現 詳細: N-His-TMV CP19 was expressed by cloning TMV common strain TMV CP gene into the Nde I and Xho I sites of pET28a vector (Novagen) for overexpression in E. coli BL21 (DE3) RIL cells (TaKaRa). ...詳細: N-His-TMV CP19 was expressed by cloning TMV common strain TMV CP gene into the Nde I and Xho I sites of pET28a vector (Novagen) for overexpression in E. coli BL21 (DE3) RIL cells (TaKaRa). Cells were grown at 37 C, with shaking at 220 rpm, in LB media supplemented with 50 g/mL kanamycin to an OD600 of 0.65, at which time protein expression was induced with 0.1 mM isopropyl-1-thio- -D-galactopyranoside (IPTG) at 16 C overnight. Cells were harvested by centrifugation and stored at -80 C until use. 由来: (組換発現) Tobacco mosaic virus (ウイルス) / 株: U1 / 遺伝子: CP / プラスミド: pET28a-N-His-TMV CP19 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (DE3) RIL / 参照: UniProt: P69687
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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: 3.29 Å3/Da / 溶媒含有率: 62.6 %
結晶化
温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.7 詳細: pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
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データ収集
回折
平均測定温度: 277 K
放射光源
由来: シンクロトロン / サイト: SSRF / ビームライン: BL17U
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
相対比: 1
反射
解像度: 3.06→50 Å / Num. obs: 155016
反射 シェル
最高解像度: 3.06 Å
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PDB_EXTRACT
3.11
データ抽出
HKL-2000
データ収集
精密化
構造決定の手法: 分子置換 / 解像度: 3.06→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.422 / SU ML: 0.279 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 1.424 / ESU R Free: 0.387 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.2547
8201
5 %
RANDOM
Rwork
0.204
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obs
0.2065
155016
99.69 %
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all
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163217
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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: 1.2 Å / 溶媒モデル: MASK