- PDB-3iee: Crystal structure of an alpha helical protein (BF3319) from Bacte... -
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基本情報
登録情報
データベース: PDB / ID: 3iee
タイトル
Crystal structure of an alpha helical protein (BF3319) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
要素
Putative exported protein
キーワード
STRUCTURAL GENOMICS (構造ゲノミクス) / UNKNOWN FUNCTION / YP_212931.1 / hypothetical protein BF3319 from Bacteroides fragilis (仮説) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
Uncharacterised protein PF12889, C-terminal DUF3829 / Uncharacterised protein PF12889, N-terminal DUF3829 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / Putative exported 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. THE CLONED CONSTRUCT CONTAINS RESIDUES 18-286 OF THE FULL LENGTH PROTEIN.
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: 0.97918 Å / 相対比: 1
反射
解像度: 1.7→29.26 Å / Num. obs: 30021 / % possible obs: 99.4 % / 冗長度: 4.8 % / Biso Wilson estimate: 18.456 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 11.1
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
1.7-1.74
4.4
0.66
1.2
9281
2089
0.66
96.1
1.74-1.79
4.8
0.585
1.3
10331
2136
0.585
99.2
1.79-1.84
4.9
0.459
1.7
10104
2083
0.459
99.5
1.84-1.9
4.9
0.388
2
9735
2000
0.388
99.1
1.9-1.96
4.9
0.295
2.6
9566
1955
0.295
99.2
1.96-2.03
4.9
0.23
3.4
9160
1880
0.23
99.4
2.03-2.11
4.9
0.183
4.2
8979
1841
0.183
99.6
2.11-2.19
4.9
0.149
5
8678
1770
0.149
99.9
2.19-2.29
4.9
0.131
5.7
8292
1695
0.131
99.7
2.29-2.4
4.9
0.117
6.2
7927
1626
0.117
99.8
2.4-2.53
4.8
0.108
6.8
7613
1570
0.108
99.8
2.53-2.69
4.9
0.098
7.4
7150
1471
0.098
99.9
2.69-2.87
4.8
0.089
8
6769
1397
0.089
99.8
2.87-3.1
4.8
0.082
8.2
6254
1298
0.082
100
3.1-3.4
4.8
0.066
9.6
5799
1207
0.066
100
3.4-3.8
4.7
0.057
10.9
5244
1110
0.057
100
3.8-4.39
4.7
0.055
11.5
4581
973
0.055
100
4.39-5.38
4.6
0.057
11.4
3912
856
0.057
99.9
5.38-7.6
4.4
0.064
9.8
2932
669
0.064
100
7.6-29.26
3.9
0.046
12.2
1554
395
0.046
98.1
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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
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: 1.7→29.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 3.964 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.1 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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE ETHYLENE GLYCOL (EDO) MOLECULES FROM THE CRYO SOLUTION WERE MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.192
1517
5.1 %
RANDOM
Rwork
0.164
-
-
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obs
0.166
29976
99.18 %
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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: MASK