- PDB-2xgb: Crystal structure of Barley Beta-Amylase complexed with 2,3- epox... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 2xgb
タイトル
Crystal structure of Barley Beta-Amylase complexed with 2,3- epoxypropyl-alpha-D-glucopyranoside
要素
BETA-AMYLASE
キーワード
HYDROLASE / CARBOHYDRATE METABOLISM / GERMINATION
機能・相同性
機能・相同性情報
beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process / identical protein binding 類似検索 - 分子機能
Glycoside hydrolase, family 14B, plant / Beta-amylase active site 2. / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta 類似検索 - ドメイン・相同性
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.
1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE CRYOPROTECTANT 2,3-EPOXYPROPYL-ALPHA-D- ...1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE CRYOPROTECTANT 2,3-EPOXYPROPYL-ALPHA-D-GLUCOPYRANOSIDE (EPG): THE LIGAND WAS A MIXTURE OF TWO DIASTEREOISOMERS EPIMERIC AT THE 2 POSITION. I.E. 2R,S-2,3-EPOXYPROPYL ALPHA-D-GLUCOPYRANOSIDE. THIS WAS SOAKED INTO CRYSTALS AT 10 MM FOR 24 HOURS. ONLY THE R DIASTEREOISOMER REACTS WITH THE PROTEIN GIVING A COVALENT LINK TO ATOM OE2 OF GLU 184. THE RESULTANT COMPLEX IS 2S-2-HYDROXY-3-ALPHA-D-GLUCOPYRANOSYLOXY PROPOXY-GAMMA-CARBONYL-GLU184
配列の詳細
PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS AT 3 POSITIONS TO UNIPROTKB DATABASE ...PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS AT 3 POSITIONS TO UNIPROTKB DATABASE ENTRY P16098. THESE CHANGES WERE IDENTIFIED FROM ELECTRON DENSITY MAPS.
-
実験情報
-
実験
実験
手法: X線回折 / 使用した結晶の数: 1
-
試料調製
結晶
マシュー密度: 1.91 Å3/Da / 溶媒含有率: 35.6 % / 解説: NONE
結晶化
温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5 詳細: CRYSTALS WERE GROWN AT 291 K USING THE HANGING DROP VAPOUR DIFFUSION METHOD WITH PROTEIN AT 10 MG PER ML AND A PRECIPITANT COMPRISED OF 14 PERCENT PEG 3350 IN 100 MM BIS-TRIS PROPANE BUFFER AT PH 5.5
解像度: 1.2→33.168 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.833 / SU ML: 0.017 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.034 / 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
0.1407
6823
5.08 %
RANDOM
Rwork
0.1167
-
-
-
obs
0.118
135435
95.922 %
-
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 BULK SOLVENT