- PDB-3fse: Crystal structure of a two-domain protein containing dj-1/thij/pf... -
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IDまたはキーワード:
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基本情報
登録情報
データベース: PDB / ID: 3fse
タイトル
Crystal structure of a two-domain protein containing dj-1/thij/pfpi-like and ferritin-like domains (ava_4496) from anabaena variabilis atcc 29413 at 1.90 A resolution
要素
two-domain protein containing DJ-1/ThiJ/PfpI-like and ferritin-like domains
キーワード
HYDROLASE / 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
Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Ferritin, core subunit, four-helix bundle / Ferritin / Class I glutamine amidotransferase-like / Ferritin-like / Ferritin-like superfamily ...Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Ferritin, core subunit, four-helix bundle / Ferritin / Class I glutamine amidotransferase-like / Ferritin-like / Ferritin-like 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
A: two-domain protein containing DJ-1/ThiJ/PfpI-like and ferritin-like domains B: two-domain protein containing DJ-1/ThiJ/PfpI-like and ferritin-like domains ヘテロ分子
AUTHORS STATE THAT ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION
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.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 2.08 Å3/Da / 溶媒含有率: 40.79 % 解説: THE AND R MERGE VALUES STATISTICS REPORTED HERE ARE BASED ON TREATING FRIEDEL PAIRS AS SEPARATE REFLECTIONS
タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2008年10月11日 / 詳細: Adjustable focusing mirrors in K-B geometry
放射
モノクロメーター: Si(111) Double Crystal Monochrometer 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: 0.97953 Å / 相対比: 1
反射
解像度: 1.9→29.975 Å / Num. obs: 52666 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.913 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 8.92
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
1.9-1.97
0.507
1.5
19377
10293
1
98
1.97-2.05
0.357
2.2
19384
10124
1
98
2.05-2.14
0.25
3.2
18153
9469
1
96.7
2.14-2.25
0.168
4.6
18487
9660
1
96.3
2.25-2.39
0.128
5.9
19139
9953
1
97.2
2.39-2.58
0.091
8
19828
10287
1
97.8
2.58-2.84
0.064
10.7
19423
10044
1
97.7
2.84-3.25
0.047
14.2
19187
9908
1
97.4
3.25-4.08
0.034
18.6
19076
9805
1
97.2
4.08-29.975
0.03
20.5
19575
10032
1
97.1
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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
XSCALE
データスケーリング
PDB_EXTRACT
3.006
データ抽出
XDS
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: 1.9→29.975 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.944 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.144 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. RESIDUE CYS 111 SEEMS PARTIALLY OXIDIZED AND COULD BE FUNCTIONALLY RELEVANT.
Rfactor
反射数
%反射
Selection details
Rfree
0.219
2676
5.1 %
RANDOM
Rwork
0.176
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obs
0.178
52664
99.41 %
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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