- PDB-3es4: Crystal structure of Protein of unknown function (DUF861) with a ... -
+
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: 3es4
タイトル
Crystal structure of Protein of unknown function (DUF861) with a RmlC-like cupin fold (17741406) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.64 A resolution
要素
uncharacterized protein DUF861 with a RmlC-like cupin fold
キーワード
structural genomics / unknown function / 17741406 / Protein of unknown function (DUF861) with a RmlC-like cupin fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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.
モノクロメーター: Double crystal monochromator / 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: 0.97921 Å / 相対比: 1
反射
解像度: 1.64→29.285 Å / Num. obs: 34348 / % possible obs: 99.5 % / 冗長度: 7.3 % / Biso Wilson estimate: 17.626 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 5.927
反射 シェル
Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.64-1.68
5.1
0.371
2.1
12258
2419
0.371
94.3
1.68-1.73
6.1
0.323
2.3
14995
2478
0.323
99.4
1.73-1.78
7.6
0.277
2.7
18187
2406
0.277
100
1.78-1.83
7.6
0.219
3.4
18020
2364
0.219
100
1.83-1.89
7.6
0.184
4
17168
2265
0.184
100
1.89-1.96
7.6
0.155
4.5
16641
2194
0.155
100
1.96-2.03
7.6
0.134
5
16312
2135
0.134
100
2.03-2.12
7.6
0.12
5.7
15738
2061
0.12
100
2.12-2.21
7.7
0.11
6.1
15123
1966
0.11
100
2.21-2.32
7.6
0.104
6.5
14204
1858
0.104
100
2.32-2.44
7.7
0.1
6.8
13803
1793
0.1
100
2.44-2.59
7.7
0.094
7.1
12979
1683
0.094
100
2.59-2.77
7.7
0.091
7.3
12194
1584
0.091
100
2.77-2.99
7.7
0.083
7.8
11351
1476
0.083
100
2.99-3.28
7.6
0.075
8.6
10272
1347
0.075
100
3.28-3.67
7.6
0.063
10.5
9347
1236
0.063
100
3.67-4.23
7.5
0.057
11.3
8050
1075
0.057
100
4.23-5.19
7.4
0.055
11.9
6804
920
0.055
100
5.19-7.33
7.4
0.072
8.8
5180
703
0.072
100
7.33-29.285
7.3
0.064
10.1
2796
385
0.064
98.9
-
位相決定
位相決定
手法: 単波長異常分散
-
解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
SCALA
3.2.5
データスケーリング
PDB_EXTRACT
3.006
データ抽出
MOSFLM
データ削減
SHARP
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 1.64→29.285 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.393 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.07 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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (4). CL ION AND 1,2-ETHYLENE GLYCOL(EDO) FROM EITHER CRYSTALLIZATION BUFFER OR CRYO SOLUTION WERE MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.16
1735
5.1 %
RANDOM
Rwork
0.142
-
-
-
obs
0.143
34317
99.53 %
-
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: MASK