- PDB-3rh2: Crystal structure of a TetR-like transcriptional regulator (Sama_... -
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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: 3rh2
タイトル
Crystal structure of a TetR-like transcriptional regulator (Sama_0099) from Shewanella amazonensis SB2B at 2.42 A resolution
要素
Hypothetical TetR-like transcriptional regulator
キーワード
DNA BINDING PROTEIN / DNA/RNA-binding 3-helical bundle / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-Biology
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 3.76 Å3/Da / 溶媒含有率: 67.31 % 解説: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND
解像度: 2.42→29.118 Å / Num. obs: 15161 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 70.116 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 7.82
反射 シェル
Rmerge(I) obs: 0.025 / Diffraction-ID: 1
解像度 (Å)
最高解像度 (Å)
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.42-2.51
1.5
16056
2905
99.8
2.51-2.61
2
15443
2780
99.6
2.61-2.72
2.9
14221
2567
99.8
2.72-2.87
4
16046
2912
99.7
2.87-3.05
5.8
15394
2803
99.9
3.05-3.28
7.7
14812
2728
99.9
3.28-3.61
10.6
14738
2811
99.8
3.61-4.13
13
14705
2825
99.9
4.13-5.19
14.8
14143
2764
99.9
5.19
15.8
14833
2822
98.4
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位相決定
位相決定
手法: 多波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
MolProbity
3beta29
モデル構築
PDB_EXTRACT
3.1
データ抽出
SHELX
位相決定
SHARP
位相決定
XSCALE
December6, 2010
データスケーリング
REFMAC
5.5.0110
精密化
XDS
データ削減
SHELXD
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.42→29.118 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 14.68 / SU ML: 0.164 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.221 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.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...詳細: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.PHOSPHATE (PO4) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE LIGAND-BINDING SITE.
Rfactor
反射数
%反射
Selection details
Rfree
0.2496
762
5 %
RANDOM
Rwork
0.2047
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obs
0.2068
15113
99.74 %
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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