- PDB-4lqx: Crystal structure of a TENA/THI-4 domain-containing protein (SSO2... -
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基本情報
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データベース: PDB / ID: 4lqx
タイトル
Crystal structure of a TENA/THI-4 domain-containing protein (SSO2700) from Sulfolobus solfataricus P2 at 2.34 A resolution
要素
TENA/THI-4 domain-containing protein
キーワード
OXIDOREDUCTASE / Two domains protein / N-terminal is prokaryotic zinc finger domain and C-terminal is TENA_THI-4 domain (PF03070) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
モノクロメーター: single crystal Si(111) bent / 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
0.97871
1
2
0.91837
1
反射
解像度: 2.34→44.628 Å / Num. obs: 33079 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.899 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.86
反射 シェル
Diffraction-ID: 1
解像度 (Å)
最高解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.34-2.42
0.767
1.7
10397
3149
98.8
2.42-2.52
0.641
2.1
10463
3260
94.7
2.52-2.63
0.493
2.7
10981
3152
98.2
2.63-2.77
0.366
3.6
11604
3347
98
2.77-2.95
0.27
4.8
11629
3389
98.2
2.95-3.17
0.179
6.8
10603
3213
98.2
3.17-3.49
0.108
10.5
11004
3276
96
3.49-3.99
0.064
17
11584
3352
99.2
3.99-5.02
0.045
21.9
10855
3368
97.3
5.02
0.039
25
11431
3568
97.5
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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
July4, 2012
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: 2.34→44.628 Å / Cor.coef. Fo:Fc: 0.9482 / Cor.coef. Fo:Fc free: 0.9237 / Occupancy max: 1 / Occupancy min: 0.37 / 交差検証法: THROUGHOUT / σ(F): 0 詳細: 1. 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 ...詳細: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 4.SO4, CL AND EDO MODELED WERE PRESENT IN PROTEIN/CYRO CONDITIONS. ZINC IONS WERE ASSIGNED BASED ON AN ANOMALOUS DIFFERENCE FOURIER MAP AND X-RAY FLUORESCENCE MEASUREMENTS. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED IN EACH CHAIN. BASED ON ELECTRON DENSITY AND INTERACTION ENVIRONMENTS THE COMPOUND MAY BE NITROBENZENE, BENZOIC ACID, NICOTINIC ACID, NICOTINAMIDE OR SOME OTHER SIMILAR COMPOUND. THE DATA ARE INSUFFICIENT TO DISTINGUISH BETWEEN THESE AND THE TRUE IDENTITY THE LIGAND IS UNKNOWN. 6. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.