- PDB-4jgl: Crystal structure of a streptavidin-like protein (BACEGG_01519) f... -
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基本情報
登録情報
データベース: PDB / ID: 4jgl
タイトル
Crystal structure of a streptavidin-like protein (BACEGG_01519) from Bacteroides eggerthii DSM 20697 at 1.25 A resolution
要素
hypothetical protein
キーワード
Structural Genomics / Unknown Function / an orphan / streptavidin-like fold with two extra alpha helices / 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 RESIDUES 24-191 OF THE TARGET SEQUENCE.
解像度: 1.25→28.331 Å / Num. all: 49718 / Num. obs: 49718 / % possible obs: 100 % / 冗長度: 11 % / Rsym value: 0.097 / Net I/σ(I): 12.6
反射 シェル
Rmerge(I) obs: 0.014 / Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.25-1.28
10.9
0.5
39805
3645
1.371
100
1.28-1.32
11
0.7
39307
3584
1.081
100
1.32-1.36
11
0.8
37919
3457
0.914
100
1.36-1.4
11
1
36901
3358
0.752
100
1.4-1.44
11
1.2
36161
3293
0.599
100
1.44-1.49
11
1.6
34528
3131
0.442
100
1.49-1.55
11
2.2
33728
3055
0.335
100
1.55-1.61
11.1
2.9
32678
2956
0.251
100
1.61-1.69
11
3.7
31066
2814
0.198
100
1.69-1.77
11
4.5
29888
2706
0.161
100
1.77-1.86
11
5.5
28137
2549
0.128
100
1.86-1.98
11
6.5
27025
2455
0.104
100
1.98-2.11
10.9
7
24841
2271
0.095
100
2.11-2.28
10.8
7.9
23338
2158
0.083
100
2.28-2.5
10.6
8
20771
1955
0.079
100
2.5-2.8
10.2
8.4
18133
1782
0.074
100
2.8-3.23
11.2
8.8
17627
1574
0.068
100
3.23-3.95
11.6
11
15502
1340
0.055
100
3.95-5.59
11.5
11.5
12005
1045
0.052
100
5.59-28.331
10.9
9.1
6430
590
0.064
99.1
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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
SCALA
3.3.20
データスケーリング
REFMAC
5.5.0110
精密化
MOSFLM
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: 1.25→28.331 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.104 / SU ML: 0.021 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.035 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. CALCIUM IONS (CA) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 4. AN UNKNOWN LIAGAND (UNL) HAS BEEN MODELED AT THE SURFACE OF THE PROTEIN BASED ON THE ELECTRON DENSITY. THE DENSITY RESEMBLES NITROBENZENE (NBZ), BENZOIC ACID (BEZ) AND NICOTINIC ACID (NIO). THE EXACT CHEMICAL SPECIES COULD NOT BE DETERMINED WITH THE AVAILABLE DATA.
Rfactor
反射数
%反射
Selection details
Rfree
0.153
2515
5.1 %
RANDOM
Rwork
0.134
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-
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obs
0.135
49663
99.95 %
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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