[phenixbb] how to make covelent link of BME with Cys and refine

Rajeshwer Sankhala Rajeshwer.Sankhala at jefferson.edu
Fri Feb 15 14:04:13 PST 2013


Hello Nat,



Thank you so much for your suggestion. I  did run phenix refinement in nightly build phenix version with "

intra_chain = True " command. This time refinement worked but again in out put pdb no disulfide bond is estabilished between cys and BME. I provided .pdb, .mtz and .cif files as input. Well can you please suggest me how i can provide both BME and Cys-BME (SS bond) restrains in .cif file? if that happens then i feel refinement should work. I am attaching my .cis file below please have a look and tell me if anything wrong with this?



BME.cif



# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.8.1-1168 (Mon Sep 28 16:48:00 2012)
#   - file written: Sat Jan 26 17:25:31 2013
#
#   Input file: Ref226_154-331-VLD2-BME.pdb
#   Random seed: 3628800
#   Residue: BME
#
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
BME        BME 'Unknown                  ' ligand 10 4 .
#
data_comp_BME
#
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
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
BME         S      S   S2    .        -19.3229  -20.3986   17.2400
BME         H5     H   H     .        -18.1988  -20.0550   17.0819
BME         C1     C   CH2   .        -19.3558  -21.8852   18.1928
BME         H3     H   HCH2  .        -18.8480  -21.7572   19.0093
BME         H4     H   HCH2  .        -18.9637  -22.6079   17.6781
BME         C      C   CH2   .        -20.7668  -22.2261   18.5333
BME         H1     H   HCH2  .        -21.1200  -21.5643   19.1482
BME         H2     H   HCH2  .        -20.7965  -23.1021   18.9488
BME         O      O   OH1   .        -21.5280  -22.2370   17.3822
BME         H      H   HOH1  .        -22.3435  -22.5247   17.5704
#
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
BME   S       H5    single        1.186 0.020
BME   S       C1    single        1.766 0.020
BME   C1      H3    single        0.970 0.020
BME   C1      H4    single        0.970 0.020
BME   C1      C     single        1.491 0.020
BME   C       H1    single        0.970 0.020
BME   C       H2    single        0.970 0.020
BME   C       O     single        1.380 0.020
BME   O       H     single        0.885 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
BME   C1      S       H5          109.48 3.000
BME   C       C1      H4          109.47 3.000
BME   C       C1      H3          109.47 3.000
BME   H4      C1      H3          109.47 3.000
BME   C       C1      S           109.47 3.000
BME   H4      C1      S           109.47 3.000
BME   H3      C1      S           109.47 3.000
BME   O       C       H2          109.47 3.000
BME   O       C       H1          109.47 3.000
BME   H2      C       H1          109.47 3.000
BME   O       C       C1          109.47 3.000
BME   H2      C       C1          109.47 3.000
BME   H1      C       C1          109.47 3.000
BME   H       O       C           109.48 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
BME Var_01         O       C       C1      S            52.25  30.0 3
BME Var_02         H1      C       C1      S           -67.75  30.0 3
BME Var_03         H2      C       C1      S           172.25  30.0 3
BME Var_04         O       C       C1      H3          172.25  30.0 3
BME Var_05         O       C       C1      H4          -67.75  30.0 3
#
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
CYS-BME  CYS      DEL-HG   .        BME   DEL-HS     .  SS-bridge
#





Thanks


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