- PDB-3dxq: Crystal structure of choline/ethanolamine kinase family protein (... -
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基本情報
登録情報
データベース: PDB / ID: 3dxq
タイトル
Crystal structure of choline/ethanolamine kinase family protein (NP_106042.1) from MESORHIZOBIUM LOTI at 2.55 A resolution
要素
choline/ethanolamine kinase family protein
キーワード
TRANSFERASE / NP_106042.1 / choline/ethanolamine kinase family protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Phosphotransferase enzyme family
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: 2.63 Å3/Da / 溶媒含有率: 53.23 %
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: 6.8 詳細: 0.2000M NaNO3, 20.0000% PEG-3350, No Buffer pH 6.8, 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
0.97882
1
2
0.97949
1
3
0.91837
1
反射
解像度: 2.55→29.566 Å / Num. obs: 23913 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 61.65 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.09
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
2.55-2.64
0.682
1.4
8249
4111
93.3
2.64-2.75
0.525
1.9
9165
4526
97.6
2.75-2.87
0.386
2.5
8688
4223
98.1
2.87-3.02
0.281
3.5
9225
4397
98.7
3.02-3.21
0.186
5.2
9340
4417
98.4
3.21-3.46
0.11
8.3
9557
4445
98.6
3.46-3.8
0.062
13
9421
4359
98.8
3.8-4.35
0.042
17.7
9617
4472
98.7
4.35-5.46
0.035
20.3
9442
4410
99
5.46
0.025
25.9
9755
4495
98
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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
5.2.0019
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
3.004
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: 多波長異常分散 / 解像度: 2.55→29.566 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.893 / SU B: 25.763 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.609 / ESU R Free: 0.328 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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
Rfactor
反射数
%反射
Selection details
Rfree
0.284
1222
5.1 %
RANDOM
Rwork
0.242
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obs
0.244
23862
99.28 %
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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