- PDB-3ge6: CRYSTAL STRUCTURE OF A PUTATIVE NITROREDUCTASE IN COMPLEX WITH FM... -
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基本情報
登録情報
データベース: PDB / ID: 3ge6
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE NITROREDUCTASE IN COMPLEX WITH FMN (EXIG_2970) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.85 A RESOLUTION
要素
Nitroreductase
キーワード
OXIDOREDUCTASE / PUTATIVE NITROREDUCTASE IN COMPLEX WITH FMN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
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 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: 2.14 Å3/Da / 溶媒含有率: 42.65 %
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: 4.6 詳細: 0.2000M NH4H2PO3, 20.0000% PEG-3350, No Buffer pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
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: 0.97982 Å / 相対比: 1
反射
解像度: 1.85→29.185 Å / Num. obs: 35856 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.089 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.79
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
1.85-1.92
0.578
1.5
13181
6970
1
97.5
1.92-1.99
0.434
2
11710
6152
1
98.5
1.99-2.08
0.347
2.5
12839
6732
1
98.6
2.08-2.19
0.24
3.5
12799
6696
1
98.8
2.19-2.33
0.2
4.2
13166
6874
1
98.4
2.33-2.51
0.149
5.4
12983
6741
1
99
2.51-2.76
0.11
6.9
12958
6709
1
99
2.76-3.16
0.078
9.3
13133
6770
1
99
3.16-3.98
0.044
14.2
13075
6740
1
98.7
3.98-29.185
0.033
18.1
13119
6734
1
98.2
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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: 1.85→29.185 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.919 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.135 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 RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. A FLAVIN MONONUCLEOTIDE (FMN) MOLECULE IS MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH SUBUNIT. THE FMN RESTRAINTS WERE CHANGED TO ALLOW BENDING OF THE ISOALLOXAZINE RING ALONG THE N5-N10 VIRTUAL AXIS RESULTING IN AN IMPROVED FIT BETWEEN THE FMN COORDINATES AND ELECTRON DENSITY.
Rfactor
反射数
%反射
Selection details
Rfree
0.213
1791
5 %
RANDOM
Rwork
0.169
-
-
-
obs
0.171
35802
99.61 %
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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