- PDB-3c8w: Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.... -
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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: 3c8w
タイトル
Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.60 A resolution
要素
Acetoacetate decarboxylase ADC
キーワード
LYASE / YP_094708.1 / acetoacetate decarboxylase (ADC) / 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 (0) FOLLOWED BY THE TARGET SEQUENCE.
モノクロメーター: Single crystal Si(111) bent (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
0.91837
1
2
0.97901
1
反射
解像度: 1.6→29.683 Å / Num. obs: 142031 / % possible obs: 80.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.188 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.27
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
1.6-1.66
0.622
1.4
37600
20973
1
66.3
1.66-1.72
0.58
1.8
48607
19568
1
71.3
1.72-1.8
0.51
2.3
80264
25102
1
80.5
1.8-1.9
0.398
3
87996
26597
1
83.2
1.9-2.02
0.273
4.5
84050
25376
1
83.6
2.02-2.17
0.193
6.3
81451
24555
1
84
2.17-2.39
0.132
9.1
85169
25700
1
84.2
2.39-2.73
0.09
13
84202
25395
1
84.6
2.73-3.44
0.046
23.4
86071
25973
1
84.9
3.44-29.683
0.023
43.1
85703
26005
1
85
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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
5.4.0067
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
データ抽出
MAR345
CCD
データ収集
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: 1.6→29.683 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.793 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096 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. THE ELECTRON DENSITY REVEALS THAT LYSINE 125 HAS FORMED A SCHIFF BASE. IT WAS MODELED AS THE ENZYME-ACETOACETATE SCHIFF BASE INTERMEDIATE, WHICH IS CONSISTENT WITH THE OBSERVED ELECTRON DENSITY AND THE PUTATIVE ENZYMATIC MECHANISM. 5. CITRATE ANIONS FROM CRYSTALLIZATION ARE MODELED IN THIS STRUCTURE. 6. POOR ELECTRON DENSITY AROUND RESIDUE 11, 12 AND 13 IN EACH SUBUNIT RESULTS IN RAMACHANDRAN OUTLIERS.
Rfactor
反射数
%反射
Selection details
Rfree
0.228
7169
5 %
RANDOM
Rwork
0.193
-
-
-
obs
0.195
142031
93.04 %
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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