- PDB-2okc: Crystal structure of Type I restriction enzyme StySJI M protein (... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 2okc
タイトル
Crystal structure of Type I restriction enzyme StySJI M protein (NP_813429.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution
要素
Type I restriction enzyme StySJI M protein
キーワード
TRANSFERASE / NP_813429.1 / N-6 DNA Methylase / Type I restriction enzyme StySJI M protein / 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
N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding 類似検索 - 分子機能
N6 adenine-specific DNA methyltransferase, N-terminal domain / : / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Ferritin ...N6 adenine-specific DNA methyltransferase, N-terminal domain / : / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Ferritin / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
ISOPROPYL ALCOHOL / S-ADENOSYLMETHIONINE / Type I restriction enzyme BthVORF4518P methylase subunit 類似検索 - 構成要素
BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999
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 FOLLOWED BY THE TARGET SEQUENCE. THE CONSTRUCT IS TRUNCATED TO EXPRESS 1-444.
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
0.97899
1
3
0.97935
1
反射
解像度: 2.2→28.62 Å / Num. obs: 46716 / % possible obs: 88.9 % / 冗長度: 3.97 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.63
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Diffraction-ID
% possible all
2.2-2.28
0.378
2.2
17760
1
86.2
2.28-2.37
0.324
2.6
18322
1
90.9
2.37-2.48
0.259
3.3
18962
1
90.8
2.48-2.61
0.208
4.1
18522
1
90.3
2.61-2.77
0.147
6
18283
1
90.3
2.77-2.98
0.101
8.4
18433
1
90
2.98-3.28
0.064
12.6
18829
1
88.9
3.28-3.76
0.04
19.8
18921
1
88.7
3.76-4.72
0.027
26.8
18603
1
88.1
4.72-28.6
0.021
31.3
18610
1
85.3
-
位相決定
位相決定
手法: 多波長異常分散
-
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
SOLVE
位相決定
REFMAC
5.2.0005
精密化
XSCALE
データスケーリング
PDB_EXTRACT
2
データ抽出
XDS
データ削減
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.2→28.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.486 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.214 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. S-ADENOSYLMETHIONINES WERE MODELED BASED ON PROPOSED FUNCTION AND STRUCTURAL HOMOLOGS. 5. CHLORINE, GLYCEROL AND 2- PROPANOL WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 6. RAMACHANDRAN OUTLIERS A124 AND B9 HAVE WEAK ELECTRON DENSITY. 7. RESIDUES A1-8, A197, A434-444, B1-6, AND B433-444 ARE IN DISORDERED REGIONS AND WERE NOT MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.232
2367
5.1 %
RANDOM
Rwork
0.182
-
-
-
obs
0.185
46612
91.8 %
-
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