- PDB-3eo6: Crystal structure of protein of unknown function (DUF1255) (AFE_2... -
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基本情報
登録情報
データベース: PDB / ID: 3eo6
タイトル
Crystal structure of protein of unknown function (DUF1255) (AFE_2634) from ACIDITHIOBACILLUS FERROOXIDANS NCIB8455 at 0.97 A resolution
要素
protein of unknown function (DUF1255)
キーワード
structural genomics / unknown function / AFE_2634 / protein of unknown function (DUF1255) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
(1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...(1) 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. (2) THE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT-KB DATABASE AT THE TIME OF DEPOSITION. IT IS AVAILABLE AS LOCUS ID AFE_2634 FROM THE COMPREHENSIVE MICROBIAL RESOURCE AT THE J. CRAIG VENTER INSTITUTE.
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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: 40.74 %
結晶化
温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: 0.2000M MgCl2, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
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
0.97837
1
反射
解像度: 0.97→28.194 Å / Num. obs: 111566 / % possible obs: 99.4 % / 冗長度: 4.1 % / Biso Wilson estimate: 7.317 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 5.911
反射 シェル
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
0.97-1
3.5
0.703
1.1
28853
8165
0.703
98
1-1.02
3.6
0.516
1.5
28209
7943
0.516
98.3
1.02-1.05
3.6
0.38
2
27510
7736
0.38
98.5
1.05-1.08
3.6
0.289
2.6
26704
7468
0.289
98.9
1.08-1.12
3.6
0.209
3.6
26350
7343
0.209
99.1
1.12-1.16
3.6
0.161
4.6
25741
7133
0.161
99.3
1.16-1.2
3.6
0.142
5.1
24913
6885
0.142
99.6
1.2-1.25
3.6
0.133
5.3
23997
6600
0.133
99.7
1.25-1.31
3.7
0.122
5.7
23315
6385
0.122
99.9
1.31-1.37
3.7
0.108
6.4
22373
6096
0.108
100
1.37-1.45
3.7
0.093
7.3
21418
5803
0.093
100
1.45-1.53
3.7
0.079
8.5
20393
5504
0.079
100
1.53-1.64
3.7
0.071
9.1
19249
5145
0.071
100
1.64-1.77
4.2
0.07
9.1
19923
4787
0.07
100
1.77-1.94
4.9
0.073
8.4
21761
4457
0.073
100
1.94-2.17
6.3
0.062
9.9
25191
3994
0.062
100
2.17-2.5
7.4
0.062
10.6
26344
3541
0.062
100
2.5-3.07
7.5
0.054
11.5
22405
3001
0.054
100
3.07-4.34
6.8
0.048
12.9
15844
2321
0.048
99.9
4.34-28.94
6.2
0.05
12.7
7749
1259
0.05
97.1
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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
5.5.0053
精密化
PHENIX
精密化
SHARP
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
精密化
構造決定の手法: 多波長異常分散 / 解像度: 0.97→28.194 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / Occupancy max: 1 / Occupancy min: 0.11 / SU B: 0.613 / SU ML: 0.015 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022 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 ~0.8 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. U VALUES WERE REFINED INDIVIDUALLY 4. TRIS (TRS) AND MG MODELED WERE PRESENT IN CRYSTALLIZATION CONDITIONS. 5. THE DENSITY FOR N-TERMINUS AND C-TERMINUS ARE POOR.
Rfactor
反射数
%反射
Selection details
Rfree
0.143
5605
5 %
RANDOM
Rwork
0.123
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obs
0.124
111533
99.36 %
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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