Dear all,
I am currently refining the structure of a protein-DNA complex using Refmac.
However, one DNA strand of the dsDNA contains one unusual nucleotide, namely
2`-deoxyuridine ("Ud") which is not defined in the standard Refmac library.
How can I tell Refmac to refine the modified nucleotide "Ud" within the DNA
strand correctly?
I`ve set up a .cif file for the monomer "Ud" derived from the .cif files of
the other deoxy-nucleotides (see below), but the phosphodiester bond between
the "Ud" nucleotide and the adjacent nucleotide on the 3` side is broken by
Refmac. Probably another .cif file has to be modified as well, but which one??
Does anyone know how to tell Refmac to make a correct phosphodiester bond
between the "Ud" residue and the 3` adjacent nucleotide?
(If possible, I would like to avoid changes in the general library file
"mon_lib_com.cif". The file "mon_lib_com.cif" contains the chemical structure
of links between polymers (e.g. cis- and trans-peptide bonds, disulfide
bridges, glycosidic bonds for sugars, phosphate bridges for DNA)).
Thanks in advance, kind regards
Kristina
Ud.cif:
global_
_lib_name mon_lib
_lib_version 4.11
_lib_update 15/04/05
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
Ud Ud '. ' . 28 19
.
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_Ud
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
Ud P P P 0.714
Ud O1P O OP -0.340
Ud O2P O OP -0.340
Ud O5* O OC2 -0.267
Ud C5* C CH2 0.066
Ud H5*1 H HCH2 0.005
Ud H5*2 H HCH2 0.005
Ud C4* C CH1 0.084
Ud H4* H HCH1 0.010
Ud O4* O O2 -0.193
Ud C1* C CH1 0.245
Ud H1* H HCH1 0.005
Ud N1 N NR6 -0.283
Ud C2 C CR6 0.448
Ud O2 O O -0.247
Ud N3 N NR16 -0.379
Ud H3 H HNR6 0.173
Ud C4 C CR6 0.286
Ud O4 O O -0.197
Ud C5 C CR16 -0.122
Ud H5 H HCR6 0.020
Ud C6 C CR16 0.168
Ud H6 H HCR6 0.020
Ud C2* C CH1 -0.043
Ud H2*1 H HCH2 0.010
Ud H2*2 H HCH2 0.010
Ud C3* C CH1 0.081
Ud H3* H HCH1 0.005
Ud O3* O OC2 -0.267
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
Ud P n/a O5* START
Ud O1P P . .
Ud O2P P . .
Ud O5* P C5* .
Ud C5* O5* C4* .
Ud H5*1 C5* . .
Ud H5*2 C5* . .
Ud C4* C5* C3* .
Ud H4* C4* . .
Ud O4* C4* C1* .
Ud C1* O4* C2* .
Ud H1* C1* . .
Ud N1 C1* C2 .
Ud C2 N1 N3 .
Ud O2 C2 . .
Ud N3 C2 C4 .
Ud H3 N3 . .
Ud C4 N3 C5 .
Ud O4 C4 . .
Ud C5 C4 C6 .
Ud H5 C5 . .
Ud C6 C5 H6 .
Ud H6 C6 . .
Ud C2* C1* H2*2 .
Ud H2*1 C2* . .
Ud H2*2 C2* . .
Ud C3* C4* O3* .
Ud H3* C3* . .
Ud O3* C3* . END
Ud C2* C3* . ADD
Ud C6 N1 . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
Ud P O5* coval 1.600 0.020
Ud P O1P coval 1.480 0.020
Ud P O2P coval 1.480 0.020
Ud C1* C2* coval 1.525 0.020
Ud C2* C3* coval 1.525 0.020
Ud C3* C4* coval 1.523 0.020
Ud C3* O3* coval 1.422 0.030
Ud C4* C5* coval 1.518 0.020
Ud C4* O4* coval 1.450 0.020
Ud O4* C1* coval 1.414 0.020
Ud C5* O5* coval 1.423 0.030
Ud C5* H5*1 coval 0.980 0.020
Ud C5* H5*2 coval 0.980 0.020
Ud C4* H4* coval 0.980 0.020
Ud C1* H1* coval 0.980 0.020
Ud C2* H2*1 coval 0.980 0.020
Ud C2* H2*2 coval 0.980 0.020
Ud C3* H3* coval 0.980 0.020
Ud N1 C2 coval 1.379 0.020
Ud C2 N3 coval 1.373 0.020
Ud N3 C4 coval 1.383 0.020
Ud C4 C5 coval 1.440 0.020
Ud C5 C6 coval 1.338 0.020
Ud C6 N1 coval 1.380 0.020
Ud C2 O2 coval 1.218 0.020
Ud C4 O4 coval 1.227 0.020
Ud N1 C1* coval 1.490 0.030
Ud N3 H3 coval 0.980 0.020
Ud C5 H5 coval 0.980 0.020
Ud C6 H6 coval 0.980 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
Ud C6 N1 C2 121.300 3.000
Ud C1* N1 C2 119.350 3.000
Ud C1* N1 C6 119.350 3.000
Ud N1 C2 N3 114.800 3.000
Ud C2 N3 C4 127.000 3.000
Ud N3 C4 C5 114.800 3.000
Ud C4 C5 C6 119.200 3.000
Ud C5 C6 N1 122.800 3.000
Ud N1 C2 O2 123.200 3.000
Ud N3 C2 O2 122.000 3.000
Ud N3 C4 O4 119.800 3.000
Ud C5 C4 O4 125.400 3.000
Ud N1 C1* O4* 108.400 3.000
Ud N1 C1* C2* 113.500 3.000
Ud C2 N3 H3 116.500 3.000
Ud C4 N3 H3 116.500 3.000
Ud C4 C5 H5 121.200 3.000
Ud C6 C5 H5 121.200 3.000
Ud C5 C6 H6 118.600 3.000
Ud N1 C6 H6 118.600 3.000
Ud O4* C1* C2* 106.400 3.000
Ud C1* C2* C3* 101.600 3.000
Ud C2* C3* C4* 102.400 3.000
Ud C2* C3* O3* 111.500 3.000
Ud O3* C3* C4* 110.000 3.000
Ud C3* C4* C5* 114.900 3.000
Ud C3* C4* O4* 105.400 3.000
Ud O4* C4* C5* 109.400 3.000
Ud C4* O4* C1* 109.700 3.000
Ud C4* C5* O5* 110.800 3.000
Ud C5* O5* P 120.000 3.000
Ud O5* P O1P 109.000 3.000
Ud O1P P O2P 120.000 3.000
Ud O5* P O2P 108.000 3.000
Ud C1* C2* O2* 110.200 3.000
Ud O2* C2* C3* 112.400 3.000
Ud O5* C5* H5*1 109.000 3.000
Ud O5* C5* H5*2 109.000 3.000
Ud C4* C5* H5*1 109.000 3.000
Ud C4* C5* H5*2 109.000 3.000
Ud H5*1 C5* H5*2 109.000 3.000
Ud C5* C4* H4* 109.000 3.000
Ud O4* C4* H4* 109.000 3.000
Ud C3* C4* H4* 109.000 3.000
Ud O4* C1* H1* 109.000 3.000
Ud C2* C1* H1* 109.000 3.000
Ud N1 C1* H1* 109.000 3.000
Ud C1* C2* H2*1 109.000 3.000
Ud C1* C2* H2*2 109.000 3.000
Ud H2*1 C2* H2*2 109.000 3.000
Ud C4* C3* H3* 109.000 3.000
Ud C3* C2* H2*1 109.000 3.000
Ud C3* C2* H2*2 109.000 3.000
Ud C2* C3* H3* 109.000 3.000
Ud O3* C3* H3* 109.000 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
Ud beta P O5* C5* C4* 170.000 25.000 3
Ud gamma O5* C5* C4* C3* 55.000 20.000 3
Ud delta C5* C4* C3* O3* 88.000 30.000 3
Ud nu0 C4* O4* C1* C2* 13.000 40.000 3
Ud nu1 O4* C1* C2* C3* -33.000 40.000 3
Ud nu4 C5* C4* O4* C1* 137.000 40.000 3
Ud chi O4* C1* N1 C2 30.000 40.000 2
Ud CONST_01 C1* N1 C2 N3 180.000 0.000 0
Ud CONST_02 N1 C2 N3 C4 0.000 0.000 0
Ud CONST_03 C2 N3 C4 C5 0.000 0.000 0
Ud CONST_04 N3 C4 C5 C6 0.000 0.000 0
Ud CONST_05 C4 C5 C6 N1 0.000 0.000 0
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
Ud chir_01 C3* C2* O3* C4* positiv
Ud chir_02 C4* C3* O4* C5* positiv
Ud chir_03 C1* N1 O4* C2* positiv
Ud chir_05 P O5* O1P O2P both
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
Ud plan N1 0.020
Ud plan C2 0.020
Ud plan O2 0.020
Ud plan N3 0.020
Ud plan C4 0.020
Ud plan O4 0.020
Ud plan C5 0.020
Ud plan C6 0.020
Ud plan C1* 0.020
Ud plan H3 0.020
Ud plan H5 0.020
Ud plan H6 0.020
