Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from Clostridium acetobutylicum at 2.00 A resolution
要素
Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog
キーワード
LYASE / NP_348457.1 / PUTATIVE CYSTATHIONINE BETA-LYASE INVOLVED IN ALUMINUM RESISTANCE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aluminium resistance protein
ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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.
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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: 2.58 Å3/Da / 溶媒含有率: 52.26 % 解説: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
モノクロメーター: Double crystal monochromator / 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: 0.97968 Å / 相対比: 1
反射
解像度: 2→30.029 Å / Num. obs: 131295 / % possible obs: 97 % / Observed criterion σ(I): -3 / 冗長度: 3.52 % / Biso Wilson estimate: 26.888 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.52
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
2-2.07
0.346
1.6
29100
23106
1
90
2.07-2.15
0.235
2.2
29568
23497
1
92.3
2.15-2.25
0.252
2.9
36963
25746
1
95
2.25-2.37
0.222
3.8
41343
25714
1
96.9
2.37-2.52
0.19
4.9
46541
26137
1
98.6
2.52-2.71
0.15
6.8
52830
25521
1
99.3
2.71-2.99
0.102
9.5
56859
26778
1
99.4
2.99-3.42
0.06
14.5
55804
25980
1
99.6
3.42-4.3
0.035
21.6
56252
25967
1
99.4
4.3-30.029
0.029
25.4
56825
26210
1
99
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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
REFMAC
5.2.0019
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
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: 2→30.029 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.687 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.128 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.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SODIUM (NA) CATIONS AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYSTALLIZATION AND CRYOPROTECTION SOLUTIONS WERE MODELED INTO THE STRUCTURE
Rfactor
反射数
%反射
Selection details
Rfree
0.187
6601
5 %
RANDOM
Rwork
0.145
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obs
0.147
131250
99.26 %
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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