- PDB-2qiw: Crystal structure of a putative phosphoenolpyruvate phosphonomuta... -
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基本情報
登録情報
データベース: PDB / ID: 2qiw
タイトル
Crystal structure of a putative phosphoenolpyruvate phosphonomutase (ncgl1015, cgl1060) from corynebacterium glutamicum atcc 13032 at 1.80 A resolution
要素
PEP phosphonomutase
キーワード
TRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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: Single crystal Si(111) bent (horizontal focusing) 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
0.91837
1
2
0.97901
1
3
0.97935
1
反射
解像度: 1.8→29.45 Å / Num. obs: 78759 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.945 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.6
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.8-1.86
0.411
2
22993
14091
1
99.4
1.86-1.94
0.318
2.6
26413
16214
1
99.7
1.94-2.03
0.229
3.5
25177
15344
1
99.9
2.03-2.13
0.168
4.9
23210
14131
1
99.7
2.13-2.27
0.127
6.2
26198
15841
1
99.7
2.27-2.44
0.093
8.4
24339
14662
1
99.8
2.44-2.69
0.074
10.2
25670
15366
1
99.7
2.69-3.07
0.047
14.8
24893
14820
1
99.8
3.07-3.87
0.029
22.8
25808
15221
1
99.7
3.87-29.45
0.021
30.5
25985
15029
1
98.5
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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
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
3
データ抽出
MAR345
CCD
データ収集
XDS
データ削減
SHELXD
位相決定
SHARP
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→29.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.233 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. PEG 400 (PG4), HEPES (EPE), SULFATE (SO4), AND GLYCEROL (GOL) ARE PRESENT IN THE CRYSTALLIZATION CRYO BUFFER, AND HAVE BEEN MODELED INTO THE STRUCTURE. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED INTO THE PUTATIVE ACTIVE SITE ON SUBUNIT A. 6). UNEXPLAINED ELECTRON DENSITIES NEAR HIS 211 IN THE A SUBUNIT, ARG 136 IN THE A SUBUNIT, AND HIS 211 IN THE B SUBUNIT WERE NOT MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.168
3957
5 %
RANDOM
Rwork
0.144
-
-
-
obs
0.145
78697
99.81 %
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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