- PDB-4eiu: Crystal structure of a DUF3823 family protein (BACUNI_03093) from... -
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基本情報
登録情報
データベース: PDB / ID: 4eiu
タイトル
Crystal structure of a DUF3823 family protein (BACUNI_03093) from Bacteroides uniformis ATCC 8492 at 1.90 A resolution
要素
uncharacterized hypothetical protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12866 family protein / DUF3823 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
機能・相同性
機能・相同性情報
Immunoglobulin-like - #2060 / DUF3823, N-terminal / Domain of unknown function DUF3823_C / Protein of unknown function (DUF3823) N-terminal domain / Domain of unknown function (DUF3823_C) / Carboxypeptidase-like, regulatory domain / Immunoglobulin-like / Sandwich / Mainly Beta 類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein 類似検索 - 構成要素
THIS CONSTRUCT (RESIDUES 24-271) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 24-271) 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: double crystal Si(111) / 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: 0.97915 Å / 相対比: 1
反射
解像度: 1.9→29.661 Å / Num. all: 32310 / Num. obs: 32310 / % possible obs: 99.9 % / 冗長度: 11.9 % / Biso Wilson estimate: 33.31 Å2 / Rsym value: 0.095 / Net I/σ(I): 12.4
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
1.9-1.95
11.9
0.972
2.6
27977
2347
0.972
100
1.95-2
12
0.742
1.1
27244
2279
0.742
100
2-2.06
12
0.556
1.4
26558
2216
0.556
100
2.06-2.12
12
0.452
1.7
25993
2172
0.452
100
2.12-2.19
12
0.359
2.1
25150
2095
0.359
100
2.19-2.27
12
0.295
2.5
24537
2046
0.295
100
2.27-2.36
12
0.24
3.1
23417
1950
0.24
100
2.36-2.45
12
0.203
3.6
22884
1905
0.203
100
2.45-2.56
12
0.18
4.1
21839
1826
0.18
100
2.56-2.69
12
0.15
4.5
20910
1747
0.15
100
2.69-2.83
11.9
0.132
5.1
19793
1665
0.132
100
2.83-3
11.9
0.113
5.7
18905
1585
0.113
100
3-3.21
11.9
0.098
6.3
17792
1495
0.098
100
3.21-3.47
11.9
0.079
7.8
16700
1403
0.079
100
3.47-3.8
11.8
0.068
9.4
15266
1294
0.068
100
3.8-4.25
11.7
0.061
10.7
13865
1185
0.061
100
4.25-4.91
11.6
0.069
9.3
12122
1046
0.069
99.9
4.91-6.01
11.4
0.074
8.7
10347
911
0.074
100
6.01-8.5
10.9
0.072
9.2
7954
728
0.072
100
8.5-29.661
9.3
0.064
10.4
3869
415
0.064
94.9
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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
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
SCALA
3.3.20
データスケーリング
REFMAC
5.6.0117
精密化
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: 単波長異常分散 / 解像度: 1.9→29.661 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.168 / SU ML: 0.08 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106 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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.PEG200 FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.2065
1634
5.1 %
RANDOM
Rwork
0.1789
-
-
-
obs
0.1803
32242
99.88 %
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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