- PDB-2rij: Crystal structure of a putative 2,3,4,5-tetrahydropyridine-2-carb... -
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基本情報
登録情報
データベース: PDB / ID: 2rij
タイトル
Crystal structure of a putative 2,3,4,5-tetrahydropyridine-2-carboxylate n-succinyltransferase (cj1605c, dapd) from campylobacter jejuni at 1.90 A resolution
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.
SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF BOTH HEXAMER AND TRIMER AS SIGNIFICANT OLIGOMERIZATION STATES IN SOLUTION.
解像度: 1.9→29.54 Å / Num. obs: 59121 / % possible obs: 100 % / 冗長度: 7.5 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 4.1
反射 シェル
Rmerge(I) obs: 0.011 / Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.9-1.95
7.5
0.7
32463
4335
1.068
100
1.95-2
7.5
0.9
31624
4209
0.838
100
2-2.06
7.5
1.2
30914
4112
0.643
100
2.06-2.12
7.5
1.5
30060
3997
0.508
100
2.12-2.19
7.5
2
29252
3885
0.379
100
2.19-2.27
7.5
2.3
28140
3734
0.324
100
2.27-2.36
7.5
2.7
27324
3627
0.275
100
2.36-2.45
7.5
3
26519
3518
0.246
100
2.45-2.56
7.5
3.5
25032
3320
0.208
100
2.56-2.69
7.6
4.2
24437
3233
0.175
100
2.69-2.83
7.5
5.2
22857
3028
0.14
100
2.83-3
7.5
6.1
22005
2916
0.114
100
3-3.21
7.5
6.3
20368
2715
0.105
100
3.21-3.47
7.4
6.3
18830
2537
0.095
100
3.47-3.8
7.4
7.4
17253
2346
0.081
100
3.8-4.25
7.4
8.4
15819
2131
0.07
100
4.25-4.91
7.4
7.9
13975
1884
0.064
100
4.91-6.01
7.4
7.6
11856
1608
0.071
100
6.01-8.5
7.2
8.5
9213
1272
0.068
100
8.5-29.54
6.8
6.2
4835
714
0.07
97.5
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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
SCALA
データスケーリング
PDB_EXTRACT
3
データ抽出
MAR345
CCD
データ収集
MOSFLM
データ削減
SHELXD
位相決定
SHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.9→29.54 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.196 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089 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. 4. CITRATE, CL AND GLYCEROL ARE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS. 5. THERE IS UNMODELED DENSITY NEAR ARG 218.
Rfactor
反射数
%反射
Selection details
Rfree
0.185
2991
5.1 %
RANDOM
Rwork
0.156
-
-
-
obs
0.157
59119
100 %
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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
原子変位パラメータ
Biso mean: 21.932 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.28 Å2
0.64 Å2
0 Å2
2-
-
1.28 Å2
0 Å2
3-
-
-
-1.91 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.9→29.54 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2904
0
21
448
3373
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
3070
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2095
X-RAY DIFFRACTION
r_angle_refined_deg
1.55
1.989
4162
X-RAY DIFFRACTION
r_angle_other_deg
0.953
3
5173
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.982
5
413
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.637
25.354
127
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.095
15
564
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.951
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
476
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
3441
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
597
X-RAY DIFFRACTION
r_nbd_refined
0.196
0.2
612
X-RAY DIFFRACTION
r_nbd_other
0.187
0.2
2185
X-RAY DIFFRACTION
r_nbtor_refined
0.176
0.2
1489
X-RAY DIFFRACTION
r_nbtor_other
0.084
0.2
1702
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.155
0.2
318
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.232
0.2
19
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.278
0.2
80
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.222
0.2
41
X-RAY DIFFRACTION
r_mcbond_it
2.274
3
2093
X-RAY DIFFRACTION
r_mcbond_other
0.567
3
800
X-RAY DIFFRACTION
r_mcangle_it
3.005
5
3108
X-RAY DIFFRACTION
r_scbond_it
5.439
8
1217
X-RAY DIFFRACTION
r_scangle_it
7.341
11
1037
LS精密化 シェル
解像度: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.322
211
-
Rwork
0.259
4105
-
all
-
4316
-
obs
-
-
100 %
精密化 TLS
手法: refined / Origin x: -9.842 Å / Origin y: 59.41 Å / Origin z: -28.889 Å