- PDB-4d02: The crystallographic structure of Flavorubredoxin from Escherichi... -
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基本情報
登録情報
データベース: PDB / ID: 4d02
タイトル
The crystallographic structure of Flavorubredoxin from Escherichia coli
要素
ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN
キーワード
ELECTRON TRANSPORT / FDP / NITRIC OXIDE / ROO / RUBREDOXIN / FLRD
機能・相同性
機能・相同性情報
nitric oxide reductase activity / nitric oxide catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / response to nitric oxide / FMN binding / electron transfer activity / iron ion binding / protein-containing complex / identical protein binding / cytoplasm 類似検索 - 分子機能
手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: VAPOUR DIFFUSION (HANGING DROP) AT 34C (307 K) USING 1.0UL OF PROTEIN AT14 MG/ML WITH 1 UL OF CRYSTALLIZATION SOLUTION (0.2M NA-CACODYLATE PH 6.5, 0.2 M MGACETATE, 20% PEG8000).
モノクロメーター: SI(111) MONOCHROMATOR CRYSTAL / 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: 1.69841 Å / 相対比: 1
反射
解像度: 1.75→129.5 Å / Num. obs: 60074 / % possible obs: 95.5 % / Observed criterion σ(I): 1.64 / 冗長度: 14.2 % / Biso Wilson estimate: 23.03 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.4
反射 シェル
解像度: 1.75→1.86 Å / 冗長度: 5.6 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.64 / % possible all: 75.4
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解析
ソフトウェア
名称
バージョン
分類
PHENIX
(PHENIX.REFINE)
精密化
XDS
データ削減
XDS
データスケーリング
SHELXCD
位相決定
SHELXE
モデル構築
精密化
構造決定の手法: 単波長異常分散 開始モデル: NONE 解像度: 1.755→129.496 Å / SU ML: 0.13 / σ(F): 1.25 / 位相誤差: 15.67 / 立体化学のターゲット値: LS_WUNIT_K1 詳細: THE REFINEMENT CONVERGED TO R- -WORK AND R-FREE OF 0.1444 AND 0.1666, RESPECTIVELY, WITH A R-FREE SET OF 5401 REFLECTIONS. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET. THE ...詳細: THE REFINEMENT CONVERGED TO R- -WORK AND R-FREE OF 0.1444 AND 0.1666, RESPECTIVELY, WITH A R-FREE SET OF 5401 REFLECTIONS. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET. THE FOLLOWING AMINOACID RESIDUES WERE MODELED WITH SIDE CHAINS IN DOUBLED CONFORMATION SER56, ARG57, LYS125, THR185, ANS217, , ARG253, VAL290, ARG339, SER357. IT WAS ONLY MODELED THE AMINOACID RESIDUES FROM 2 TO 400, BECAUSE THE RUBREDOXIN DOMAIN AT C-TERMINAL WAS NOT VISIBLE IN THE 2FO-FC MAPS. THE NATURE OF PHOSPHATE AND CHLORIDE SOLVENT MOLECULES WAS CONFIRMED BY THEIR ANOMALOUS SIGNAL.
Rfactor
反射数
%反射
Rwork
0.1407
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obs
0.1407
59089
94.31 %
Rfree
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2902
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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