- PDB-4r03: Crystal structure of a DUF3836 family protein (BDI_3222) from Par... -
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データを開く
IDまたはキーワード:
読み込み中...
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基本情報
登録情報
データベース: PDB / ID: 4r03
タイトル
Crystal structure of a DUF3836 family protein (BDI_3222) from Parabacteroides distasonis ATCC 8503 at 1.50 A resolution
要素
Uncharacterized protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12930 family protein / DUF3836 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
機能・相同性
Lipocalin - #720 / Protein of unknown function DUF3836 / Family of unknown function (DUF3836) / Lipocalin / Beta Barrel / Mainly Beta / CITRIC ACID / PHOSPHATE ION / Uncharacterized protein
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 29-136 OF THE TARGET SEQUENCE.
解像度: 1.5→27.084 Å / Num. obs: 27948 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.114 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.96
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
1.5-1.6
0.483
1.9
10277
4505
1
91.2
1.6-1.66
0.347
3.3
7844
2397
1
99.7
1.66-1.73
0.263
4.7
8912
2431
1
99.9
1.73-1.83
0.181
6.7
10443
2857
1
99.9
1.83-1.94
0.108
10.9
9033
2480
1
99.8
1.94-2.09
0.071
15.9
9457
2596
1
99.8
2.09-2.3
0.054
20.5
9552
2624
1
99.7
2.3-2.63
0.045
23.6
9395
2596
1
99.7
2.63-3.31
0.033
30.7
9500
2667
1
99.4
3.31-27.084
0.027
38
9596
2759
1
98.8
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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
MolProbity
3beta29
モデル構築
PDB_EXTRACT
3.1
データ抽出
SHELX
位相決定
SHARP
位相決定
XSCALE
January10, 2014BUILT=20140307
データスケーリング
REFMAC
5.8.0069
精密化
XDS
データ削減
SHELXD
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.5→27.084 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.175 / SU ML: 0.042 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 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. CITRATE (CIT), PHOSPHATE (PO4), AND 2-METHYL-2,4-PENTANEDIOL (MPD) WERE PRESENT IN PURIFICATION/CRYSTALLIZATION CONDITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.1876
1407
5 %
RANDOM
Rwork
0.1664
-
-
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obs
0.1675
26540
98.15 %
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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