- PDB-3oz2: Crystal structure of a geranylgeranyl bacteriochlorophyll reducta... -
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基本情報
登録情報
データベース: PDB / ID: 3oz2
タイトル
Crystal structure of a geranylgeranyl bacteriochlorophyll reductase-like (Ta0516) from Thermoplasma acidophilum at 1.60 A resolution
要素
Digeranylgeranylglycerophospholipid reductase
キーワード
Flavoprotein / oxidoreductase / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
機能・相同性
機能・相同性情報
2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H] / membrane lipid biosynthetic process / glycerophospholipid metabolic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / geranylgeranyl reductase activity / phospholipid biosynthetic process / FAD binding / NAD binding / NADP binding / plasma membrane 類似検索 - 分子機能
ジャーナル: J.Mol.Biol. / 年: 2010 タイトル: Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of ...タイトル: Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. 著者: Xu, Q. / Eguchi, T. / Mathews, I.I. / Rife, C.L. / Chiu, H.J. / Farr, C.L. / Feuerhelm, J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / Deacon, ...著者: Xu, Q. / Eguchi, T. / Mathews, I.I. / Rife, C.L. / Chiu, H.J. / Farr, C.L. / Feuerhelm, J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
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.
解像度: 1.6→45.257 Å / Num. obs: 55071 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.479 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.16
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
1.6-1.64
0.466
2.4
14404
4009
1
99.6
1.64-1.69
0.372
3
14078
3912
1
99.5
1.69-1.74
0.305
3.7
13773
3820
1
99.6
1.74-1.79
0.252
4.5
13485
3726
1
99.7
1.79-1.85
0.205
5.5
13195
3623
1
99.8
1.85-1.91
0.155
7.1
12708
3500
1
99.9
1.91-1.98
0.116
9.2
12328
3382
1
99.9
1.98-2.07
0.096
11.2
11996
3281
1
99.9
2.07-2.16
0.079
13.4
11420
3126
1
99.9
2.16-2.26
0.07
15.2
10887
2980
1
99.8
2.26-2.39
0.061
17.4
10483
2862
1
99.8
2.39-2.53
0.054
19.1
9911
2709
1
99.6
2.53-2.7
0.051
20.6
9339
2554
1
99.5
2.7-2.92
0.046
23.1
8633
2368
1
99.1
2.92-3.2
0.04
25.6
8021
2200
1
99.4
3.2-3.58
0.035
28.1
7215
1984
1
98.6
3.58-4.13
0.033
30.1
6360
1765
1
98.5
4.13-5.06
0.032
30.7
5337
1500
1
98
5.06-7.16
0.039
29.5
4104
1180
1
96.4
7.16-45.257
0.038
29.4
2120
648
1
89.4
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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
SHELX
位相決定
REFMAC
5.5.0110
精密化
XSCALE
データスケーリング
PDB_EXTRACT
3.1
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: 1.6→45.257 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.679 / SU ML: 0.046 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.074 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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. FAD IS MODELED BASED ON DENSITY AND FUNCTION. 6. A BACTERIAL LIPID FOUND IN THE ACTIVE SITE WAS TENTATIVELY ASSIGNED AS A PHOSPHATIDYLGYLCEROL (OZ2) BASED ON DENSITY AND FUNCTION. THE DENSITY FOR THE HEAD GROUP AND LIPID TAILS ARE POORLY DEFINED. 7. ETHYLENE GLYCOL (EDO) AND GLYCEROL (GOL) WERE MODELED BASED ON CRYSTALLIZATION/CYRO CONDITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.1706
2794
5.1 %
RANDOM
Rwork
0.153
-
-
-
obs
0.1539
55071
99.35 %
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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