- PDB-1vk8: CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PRO... -
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基本情報
登録情報
データベース: PDB / ID: 1vk8
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION
要素
hypothetical protein TM0486
キーワード
BIOSYNTHETIC PROTEIN / PROTEIN WITH POSSIBLE ROLE IN CELL WALL BIOGENESIS / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
機能・相同性
Thiamine-binding protein / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Unknown ligand / Thiamine_BP domain-containing protein
解像度: 1.8→41.71 Å / Num. obs: 25897 / % possible obs: 76.1 % / 冗長度: 1.9 % / Biso Wilson estimate: 24.97 Å2 / Rsym value: 0.06 / Net I/σ(I): 10.2
反射 シェル
解像度: 1.8→1.85 Å / 冗長度: 1.6 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 607 / Rsym value: 0.116 / % possible all: 23.9
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解析
ソフトウェア
名称
バージョン
分類
MOSFLM
データ削減
SCALA
4.2)
データスケーリング
SOLVE
位相決定
RESOLVE
モデル構築
REFMAC
5.1.24
精密化
CCP4
(SCALA)
データスケーリング
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: 1.8→41.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.867 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.142 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). AN UNKNOWN LIGAND IS ASSOCIATED WITH EACH OF THE 4 SUBUNITS. UNAMBIGUOUS ASSIGNMENT OF THE IDENTITY OF THIS MOIETY WAS NOT POSSIBLE, ...詳細: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). AN UNKNOWN LIGAND IS ASSOCIATED WITH EACH OF THE 4 SUBUNITS. UNAMBIGUOUS ASSIGNMENT OF THE IDENTITY OF THIS MOIETY WAS NOT POSSIBLE, THOUGH THE DENSITY CAN BE CLOSELY ACCOUNTED FOR BY A GUANINE BASE. IT IS LABELED 'UNL' AND ALL ATOMS WERE REFINED AS OXYGEN ATOMS. BUMP RESTRAINTS WERE REMOVED FOR THE REFINEMENT OF ATOMS IN EACH OF THESE LIGANDS. 3). TLS GROUPS WERE CHOSEN BY PROTEIN SUBUNIT IDENTIFICATION IN THE CRYSTALLOGRAPHIC ASSYMETRIC UNIT.
Rfactor
反射数
%反射
Selection details
Rfree
0.18956
1336
5.2 %
RANDOM
Rwork
0.14151
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obs
0.14404
24544
76.08 %
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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: BABINET MODEL WITH MASK