Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Compound details
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.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.5 Å3/Da / Density % sol: 50.89 %
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→19.74 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.441 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23267
1425
5 %
RANDOM
Rwork
0.18316
-
-
-
obs
0.18554
27088
95.86 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 27.922 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 2.03→19.74 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2859
0
82
279
3220
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.02
2996
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.131
1.98
4050
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.29
5
381
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.254
25.814
129
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.686
15
504
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.048
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.075
0.2
473
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
2227
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 refinement shell
Resolution: 2.03→2.083 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.264
77
-
Rwork
0.215
1656
-
obs
-
-
88.28 %
Refinement TLS params.
Method: refined / Origin x: 4.201 Å / Origin y: 21.5452 Å / Origin z: -14.1857 Å
11
12
13
21
22
23
31
32
33
T
0.0162 Å2
0.0003 Å2
0.0155 Å2
-
0.0341 Å2
0.0018 Å2
-
-
0.0265 Å2
L
0.0523 °2
0.0316 °2
0.0125 °2
-
0.5695 °2
0.0565 °2
-
-
0.2207 °2
S
-0.0042 Å °
0.0355 Å °
0.0088 Å °
0.0299 Å °
-0.0424 Å °
0.0815 Å °
0.0104 Å °
0.0026 Å °
0.0466 Å °
+
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