- PDB-2wmk: Crystal structure of the catalytic module of a family 98 glycosid... -
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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: 2wmk
タイトル
Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae SP3-BS71 (Sp3GH98) in complex with the A-LewisY pentasaccharide blood group antigen.
要素
FUCOLECTIN-RELATED PROTEIN
キーワード
HYDROLASE / BLOOD GROUP / ANTIGEN / FUCOSE UTILIZATION
機能・相同性
機能・相同性情報
family 98 glycoside hydrolase / arginine biosynthesis bifunctional protein fold / Polysaccharide lyase family 8-like, C-terminal / Chondroitinase Ac; Chain A, domain 3 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta 類似検索 - ドメイン・相同性
Blood group A Lewis Y antigen, beta anomer / : 類似検索 - 構成要素
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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" 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.
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose / Blood group A Lewis Y antigen / beta anomer
タイプ: oligosaccharide, Oligosaccharide / クラス: 抗原 / 分子量: 878.823 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: oligosaccharide with branches / 参照: Blood group A Lewis Y antigen, beta anomer
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: 0.9793 Å / 相対比: 1
反射
解像度: 1.9→40 Å / Num. obs: 102091 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / 冗長度: 6.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.5
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解析
ソフトウェア
名称: REFMAC / バージョン: 5.2.0019 / 分類: 精密化
精密化
構造決定の手法: OTHER 開始モデル: NONE 解像度: 1.9→29.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.594 / SU ML: 0.078 / 交差検証法: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.13 / 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
0.2096
5371
5 %
RANDOM
Rwork
0.16248
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obs
0.16481
102091
99.03 %
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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