- PDB-3ks7: Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) ... -
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基本情報
登録情報
データベース: PDB / ID: 3ks7
タイトル
Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution
要素
Putative Putative PNGase F
キーワード
HYDROLASE / Putative Peptide:N-glycosidase F (PNGase F) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
機能・相同性情報
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen 類似検索 - 分子機能
Peptide-N-glycosidase F, N-terminal domain / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal ...Peptide-N-glycosidase F, N-terminal domain / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / Jelly Rolls / Sandwich / Mainly Beta 類似検索 - ドメイン・相同性
IODIDE ION / N-glycanase_N domain-containing protein 類似検索 - 構成要素
ANALYTICAL SIZE EXCULSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
SEQUENCE: THIS CONSTRUCT (RESIDUE 20-415) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE: THIS CONSTRUCT (RESIDUE 20-415) 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 monochromator (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
0.97922
1
3
0.97876
1
反射
解像度: 2.3→29.881 Å / Num. obs: 87284 / % possible obs: 99.8 % / 冗長度: 3.7 % / Biso Wilson estimate: 43.391 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 9.9
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
2.3-2.36
3.8
0.789
1
24125
6398
0.789
99.9
2.36-2.42
3.8
0.702
1.1
23376
6227
0.702
100
2.42-2.49
3.8
0.569
1.3
22829
6071
0.569
99.9
2.49-2.57
3.8
0.486
1.6
22089
5887
0.486
100
2.57-2.66
3.8
0.373
2.1
21570
5732
0.373
99.9
2.66-2.75
3.8
0.304
2.5
20826
5532
0.304
100
2.75-2.85
3.8
0.249
3.1
20014
5327
0.249
100
2.85-2.97
3.8
0.196
3.9
19440
5172
0.196
100
2.97-3.1
3.8
0.16
4.7
18540
4934
0.16
100
3.1-3.25
3.8
0.117
6.4
17820
4746
0.117
100
3.25-3.43
3.7
0.086
8.5
16972
4533
0.086
100
3.43-3.64
3.8
0.068
10.2
15996
4260
0.068
100
3.64-3.89
3.7
0.063
10.8
15156
4046
0.063
99.9
3.89-4.2
3.7
0.059
10.8
13960
3747
0.059
99.9
4.2-4.6
3.7
0.05
12.2
12919
3473
0.05
99.8
4.6-5.14
3.7
0.046
13.6
11739
3155
0.046
99.8
5.14-5.94
3.7
0.049
13.4
10324
2792
0.049
99.6
5.94-7.27
3.7
0.05
13.4
8707
2370
0.05
99.6
7.27-10.29
3.6
0.045
13.6
6730
1862
0.045
99.2
10.29-29.88
3.4
0.041
11.5
3481
1020
0.041
93.9
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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
5.5.0102
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: 多波長異常分散 / 解像度: 2.3→29.881 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 15.772 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.219 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. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLS MOTION DETERMINATION SERVER. 4. ANOMALOUS DIFFERENCE MAPS SUPPORTED THE MODELING OF IODIDE (IOD) FROM THE CRYSTALLIZATION SOLUTION. THE OCCUPANCIES ON THE IODIDES WERE REDUCED TO ACCOUNT FOR THE OBSERVED SCATTERING. 5. ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE AND CHLORIDE (CL) FROM THE PURIFICATION/ CRYSTALLIZATION SOLUTIONS WERE MODELED INTO THE STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.237
4375
5 %
RANDOM
Rwork
0.201
-
-
-
obs
0.203
87221
99.74 %
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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: MASK