- PDB-4qy7: Crystal structure of a yobA protein (BSU18810) from Bacillus subt... -
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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: 4qy7
タイトル
Crystal structure of a yobA protein (BSU18810) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 A resolution
要素
Uncharacterized protein YobA
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF11518 family protein / DUF3221 / OB-fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
機能・相同性
Protein of unknown function DUF3221 / Protein of unknown function (DUF3221) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / Uncharacterized protein YobA
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 29-120 OF 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: 1.99 Å3/Da / 溶媒含有率: 38.15 %
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: 6 詳細: 5.00% polyethylene glycol 3000, 40.00% polyethylene glycol 400, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
解像度: 1.55→27.746 Å / Num. obs: 12907 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.025 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 14.83
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
1.55-1.61
0.521
1.6
4536
2442
1
94.5
1.61-1.67
0.409
2.2
4093
2183
1
99
1.67-1.75
0.288
3.2
4739
2492
1
99.2
1.75-1.84
0.179
4.9
4397
2309
1
99.1
1.84-1.95
0.107
8.1
4318
2275
1
99.3
1.95-2.1
0.067
12.6
4532
2372
1
99
2.1-2.31
0.042
18.4
4559
2376
1
99.4
2.31-2.65
0.032
21.9
4580
2401
1
98.7
2.65-3.33
0.02
32.3
4560
2359
1
98.6
3.33-27.746
0.016
42.8
4512
2346
1
96.4
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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
BUSTER-TNT
2.10.0
精密化
XDS
データ削減
SHELXD
位相決定
BUSTER
2.10.0
精密化
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.55→27.746 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.26 / 交差検証法: THROUGHOUT / σ(F): 0 詳細: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF ...詳細: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. 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. 5. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 6. NONAETHYLENE GLYCOL (2PE) MOLECULE FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.