THE OCTAPRENYL PYROPHOSPHATE LIGAND COPURIFIED WITH THE OVEREXPRESSED CPS2A PROTEIN AND WAS ...THE OCTAPRENYL PYROPHOSPHATE LIGAND COPURIFIED WITH THE OVEREXPRESSED CPS2A PROTEIN AND WAS DETECTED BY MASS SPECTROSCOPY; THE MASS SPECTROSCOPY DATA DO NOT RULE OUT THE PRESENCE OF OTHER POLYPRENOL PYROPHOSPHATE LIGANDS IN THE SAME BINDING SITE. THE LIGAND HAS BEEN MODELLED WITH THE SEVEN CHIRAL DOUBLE BONDS IN THE CIS CONFIGURATION, AS OCCUR IN THE EQUIVALENT DOUBLE BONDS IN THE LIPID CHAIN OF THE NATURALLY OCCURING SUBSTRATE OF THE ENZYME. THE ELECTRON DENSITY CAN ALSO ACOMMODATE DITRANSPENTACISOCTAPRENYL PYROPHOSPHATE{IUPAC NAME[(2Z,6Z,10Z,14Z,18Z,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL] PHOSPHONOHYDROGEN PHOSPHATE}, AN INTERMEDIATE IN THE SYNTHESIS OF UNDECAPRENYL PYROPHOSPHATE.
構造決定の手法: 分子置換 / 解像度: 2.05→19.73 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.515 / SU ML: 0.105 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
反射数
%反射
Selection details
Rfree
0.24207
1456
5.1 %
RANDOM
Rwork
0.19058
-
-
-
obs
0.19305
27357
99.64 %
-
all
-
28971
-
-
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: 26.407 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
0.01 Å2
0 Å2
3-
-
-
-0.02 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.05→19.73 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2849
0
73
159
3081
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.02
2985
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.285
1.981
4042
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.5
5
380
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.562
25.669
127
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.797
15
512
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.967
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
474
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2214
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS精密化 シェル
解像度: 2.05→2.103 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.293
83
-
Rwork
0.201
1787
-
obs
-
-
99.79 %
精密化 TLS
手法: refined / Origin x: -4.3042 Å / Origin y: -21.5388 Å / Origin z: -14.1745 Å