- PDB-3ege: Crystal structure of Putative methyltransferase from antibiotic b... -
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基本情報
登録情報
データベース: PDB / ID: 3ege
タイトル
Crystal structure of Putative methyltransferase from antibiotic biosynthesis pathway (YP_324569.1) from ANABAENA VARIABILIS ATCC 29413 at 2.40 A resolution
要素
Putative methyltransferase from antibiotic biosynthesis pathwayメチルトランスフェラーゼ
キーワード
TRANSFERASE (転移酵素) / YP_324569.1 / Putative methyltransferase from antibiotic biosynthesis pathway (メチルトランスフェラーゼ) / Structural Genomics (構造ゲノミクス) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Methyltransferase domain (メチルトランスフェラーゼ)
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: 0.97915 Å / 相対比: 1
反射
解像度: 2.4→29.761 Å / Num. obs: 18494 / % possible obs: 99.8 % / 冗長度: 8.7 % / Biso Wilson estimate: 48.467 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 6.022
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
2.4-2.46
5.6
0.714
1.1
7507
1335
0.714
98.7
2.46-2.53
6.8
0.647
1.1
8624
1266
0.647
99.9
2.53-2.6
8.6
0.565
1.4
11109
1287
0.565
100
2.6-2.68
9.2
0.487
1.6
11458
1240
0.487
100
2.68-2.77
9.3
0.389
2
11144
1203
0.389
100
2.77-2.87
9.3
0.333
2.3
10936
1179
0.333
100
2.87-2.98
9.3
0.259
2.9
10395
1120
0.259
100
2.98-3.1
9.2
0.187
4
10127
1095
0.187
100
3.1-3.24
9.2
0.157
4.6
9635
1043
0.157
100
3.24-3.39
9.2
0.122
6
9095
988
0.122
100
3.39-3.58
9.2
0.095
7.6
8849
967
0.095
100
3.58-3.79
9.2
0.077
9
8436
919
0.077
100
3.79-4.06
9.1
0.066
10.2
7760
854
0.066
100
4.06-4.38
9
0.064
10.1
7111
786
0.064
100
4.38-4.8
9
0.064
9.8
6728
750
0.064
100
4.8-5.37
8.9
0.068
9.5
6023
680
0.068
100
5.37-6.2
8.8
0.069
9.4
5279
602
0.069
100
6.2-7.59
8.6
0.076
8.3
4525
525
0.076
100
7.59-10.73
8.3
0.045
13
3449
414
0.045
100
10.73-29.76
7.4
0.044
12
1788
241
0.044
95.2
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位相決定
位相決定
手法: 単波長異常分散
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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
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
SHELXD
位相決定
autoSHARP
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.4→29.761 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.455 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.172 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 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. EDO MOLECULE FROM THE CRYSTALLIZATION SOLUTION IS MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.202
946
5.1 %
RANDOM
Rwork
0.182
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obs
0.184
18460
99.76 %
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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