- PDB-4puc: Crystal structure of a SusD homolog (BACUNI_02643) from Bacteroid... -
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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: 4puc
タイトル
Crystal structure of a SusD homolog (BACUNI_02643) from Bacteroides uniformis ATCC 8492 at 2.00 A resolution
要素
SusD homolog
キーワード
SUGAR BINDING PROTEIN / SusD-like family / PF12741 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 27-529 OF 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: 2.49 Å3/Da / 溶媒含有率: 50.61 %
結晶化
温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 詳細: 0.2M zinc acetate, 10.0% polyethylene glycol 8000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
モノクロメーター: single crystal Si(111) bent / プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID
波長 (Å)
相対比
1
0.91162
1
2
0.97959
1
3
0.97889
1
反射
解像度: 2→89.858 Å / Num. obs: 59887 / % possible obs: 75.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.719 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.89
反射 シェル
Diffraction-ID: 1
解像度 (Å)
最高解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2-2.05
0.547
1.4
11266
6645
61.4
2.05-2.11
0.372
1.7
2109
1381
13
2.11-2.17
0.341
2.4
17776
9904
96.5
2.17-2.24
0.3
2.7
13764
7884
79.2
2.24-2.31
0.233
3
3266
2087
21.4
2.31-2.39
0.21
3.7
16102
8988
96
2.39-2.48
0.175
4.5
16065
8810
97.3
2.48-2.58
0.15
5.3
15231
8388
97
2.58-2.7
0.136
5.8
6372
3594
43.1
2.7-2.83
0.1
7.2
12101
7254
90.8
2.83-2.98
0.079
9.3
13270
7321
96.7
2.98-3.16
0.06
11.8
12783
6970
96.7
3.16-3.38
0.046
15.2
11708
6460
96.2
3.38-3.65
0.036
18
6078
3614
57.5
3.65-4
0.031
20.7
6211
3487
60.7
4-4.47
0.027
24.6
9274
5019
95.9
4.47-5.16
0.026
25.6
7758
4304
93.5
5.16-6.32
0.029
22.9
6392
3620
93.7
6.32-8.94
0.022
27.6
5215
2883
96.3
8.94
0.015
36.4
2730
1528
92.3
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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
データスケーリング
REFMAC
5.7.0032
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→89.858 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.249 / SU ML: 0.108 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.171 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. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. ANOMALOUS DIFFERENCE FOURIERS AND PRESENCE OF ZINC ACETATE IN CRYSTALLIZATION SOLUTION SUPPORT THE MODELING OF ZINC IONS. 7. ACETATE (ACT) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 8. THE NOMINAL RESOLUTION IS 2.20 A WITH 12238 OBSERVED REFLECTIONS BETWEEN 2.20-2.00 (65.2% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
Rfactor
反射数
%反射
Selection details
Rfree
0.1998
3009
5 %
RANDOM
Rwork
0.1681
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-
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obs
0.1697
59881
78.08 %
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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: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK