- PDB-3m7a: Crystal structure of Saro_0823 (YP_496102.1) a protein of unknown... -
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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: 3m7a
タイトル
Crystal structure of Saro_0823 (YP_496102.1) a protein of unknown function from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.22 A resolution
要素
uncharacterized protein
キーワード
structural genomics / unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Uncharacterized ACR / COG1430
機能・相同性
Protein of unknown function DUF192 / Protein of unknown function DUF192 / Saro_0823-like superfamily / Uncharacterized ACR, COG1430 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta / DUF192 domain-containing protein
THIS CONSTRUCT (RESIDUES 27-165) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THIS CONSTRUCT (RESIDUES 27-165) WAS EXPRESSED WITH AN N-TERMINAL 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: 2.05 Å3/Da / 溶媒含有率: 39.91 %
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: 8.86 詳細: 29.5000% polyethylene glycol 4000, 0.2000M magnesium chloride, 0.1M TRIS pH 8.86, 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
0.97883
1
2
0.91837
1
反射
解像度: 1.22→45.531 Å / Num. obs: 71683 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 8.037 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.24
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.22-1.26
0.658
1.8
22928
6473
97.2
1.26-1.31
0.581
2.1
25656
7062
97.5
1.31-1.37
0.479
2.5
26277
7186
97.9
1.37-1.45
0.361
3.4
28955
7890
98.1
1.45-1.54
0.27
4.7
28709
7034
98.8
1.54-1.66
0.206
7.1
38913
7185
98.9
1.66-1.82
0.159
10.6
47842
6877
99.2
1.82-2.09
0.101
16.8
55059
7426
99.3
2.09-2.63
0.078
22.6
53189
7184
99.5
2.63-45.531
0.052
29.8
53509
7353
99.1
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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
5.5.0102
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
autoSHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.22→45.531 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.216 / SU ML: 0.024 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 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. ETHYLENE GLYCOL (EDO) MODELED WERE PRESENT IN CRYO CONDITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.148
3565
5 %
RANDOM
Rwork
0.117
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obs
0.119
71683
98.95 %
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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