- PDB-1vkh: CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM S... -
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基本情報
登録情報
データベース: PDB / ID: 1vkh
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION
要素
putative serine hydrolase
キーワード
HYDROLASE / PUTATIVE SERINE HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
機能・相同性
機能・相同性情報
arylformamidase / arylformamidase activity / tryptophan catabolic process to kynurenine / 'de novo' NAD biosynthetic process from tryptophan / NAD biosynthetic process / positive regulation of cell growth / hydrolase activity 類似検索 - 分子機能
SEQUENCE CLONING ARTIFACT. THE CONSTRUCT WAS PCR AMPLIFIED WITH TAQ POLYMERASE. SEQUENCING OF THE ...SEQUENCE CLONING ARTIFACT. THE CONSTRUCT WAS PCR AMPLIFIED WITH TAQ POLYMERASE. SEQUENCING OF THE CLONED CONSTRUCT INDICATED THAT VAL IN POSITION 161 WAS MUTATED TO ILE.
解像度: 1.85→50 Å / Num. obs: 42225 / % possible obs: 99.77 % / 冗長度: 3.89 % / Biso Wilson estimate: 27.53 Å2 / Rsym value: 0.069 / Net I/σ(I): 17.88
反射 シェル
解像度: 1.85→1.92 Å / 冗長度: 3.57 % / Mean I/σ(I) obs: 3.57 / Num. unique all: 4159 / Rsym value: 0.343 / % possible all: 98.39
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解析
ソフトウェア
名称
バージョン
分類
DENZO
データ削減
SCALEPACK
データスケーリング
SOLVE
位相決定
RESOLVE
モデル構築
REFMAC
5.1.9999
精密化
RESOLVE
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.85→37.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.233 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. NON-ROTOMERS: LEU 156 AND LEU 160 (MOLECULE A AND B).
Rfactor
反射数
%反射
Selection details
Rfree
0.1894
2060
5 %
RANDOM
Rwork
0.14292
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obs
0.14523
39479
100 %
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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: BABINET MODEL WITH MASK