*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
list of monomers, links and modification should be in the beginning of
the dictionary. If you have two dictionaries and you want to merge them
then it is best done using libcheck
libcheck
file_l2 <d1.file>
file_l <d2.file>
Or you can use sketcher to do this.
Garib
On 10 May 2006, at 23:10, Page, Rebecca wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
CCP4 BB,
I have two proteins that form a heterodimer and have generated a
chemical crosslink between them.
The crosslinking reagent is used to couple carboxyl groups to primary
amines. In my case, it has catalyzed the formation of a amide bond
between a glutamic acid side chain from one protein a lysine amine
side chain of the second.
I have 2.4 A data and would like to refine the model. The crosslink is
clearly visible in the electron density map.
I have tried the following:
1. Created two 'new' amino acids: GXX and LYX, which only differ from
the definitions for GLU and LYS in the atoms which are not present
because of the crosslink.
2. Created a new link called XLINK (based on the definition of the
TRANS link)
3. Put these three files into a single file which I read in when I run
refmac (attached below)
4. I have added the 'LINK' to the pdb file as well:
LINK GXX A 2 LYX B 401
XLINK
I get the following error from refmac.
ERR: item _chem_link_bond.link_id :XLINK not found in the list of
links
BLOCK :data_link_XLINK
I've included the library file I created below. It is organized like
the mon_lib.cif file and the monomer descriptions are followed by the
link descriptions. Why doesn't refmac read in the link?
Thanks in advance,
Rebecca
global_
_lib_name mon_lib_EDIT
_lib_version 4.7
_lib_update 05/10/06
# ------------------------------------------------
#
# --- 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
LYX LYX 'CROSSLINKED-LYSINE ' L-peptide
20 9 .
GXX GXX 'CROSSLINKED-GLUTAMATE ' L-peptide
14 8 .
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GXX
#
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
GXX N N NH1 -0.204
GXX H H HNH1 0.204
GXX CA C CH1 0.058
GXX HA H HCH1 0.046
GXX CB C CH2 -0.078
GXX HB1 H HCH2 0.039
GXX HB2 H HCH2 0.039
GXX CG C CH2 -0.067
GXX HG1 H HCH2 0.041
GXX HG2 H HCH2 0.041
GXX CD C C 0.318
GXX OE1 O OC -0.422
GXX C C C 0.318
GXX O O O -0.422
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
GXX N n/a CA START
GXX H N . .
GXX CA N C .
GXX HA CA . .
GXX CB CA CG .
GXX HB1 CB . .
GXX HB2 CB . .
GXX CG CB CD .
GXX HG1 CG . .
GXX HG2 CG . .
GXX OE1 CD . .
GXX C CA . END
GXX O C . .
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
GXX N H coval 0.860 0.020
GXX N CA coval 1.458 0.019
GXX CA HA coval 0.980 0.020
GXX CA CB coval 1.530 0.020
GXX CB HB1 coval 0.970 0.020
GXX CB HB2 coval 0.970 0.020
GXX CB CG coval 1.520 0.030
GXX CG HG1 coval 0.970 0.020
GXX CG HG2 coval 0.970 0.020
GXX CG CD coval 1.516 0.025
GXX CD OE1 coval 1.249 0.019
GXX CA C coval 1.525 0.021
GXX C O coval 1.231 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
GXX H N CA 114.000 3.000
GXX HA CA CB 109.000 3.000
GXX CB CA C 110.100 1.900
GXX HA CA C 109.000 3.000
GXX N CA HA 110.000 3.000
GXX N CA CB 110.500 1.700
GXX HB1 CB HB2 110.000 3.000
GXX HB2 CB CG 108.000 3.000
GXX HB1 CB CG 108.000 3.000
GXX CA CB HB1 109.000 3.000
GXX CA CB HB2 109.000 3.000
GXX CA CB CG 114.100 2.000
GXX HG1 CG HG2 110.000 3.000
GXX HG2 CG CD 108.000 3.000
GXX HG1 CG CD 108.000 3.000
GXX CB CG HG1 109.000 3.000
GXX CB CG HG2 109.000 3.000
GXX CB CG CD 112.600 1.700
GXX CG CD OE1 118.400 2.300
GXX N CA C 111.200 2.800
GXX CA C O 120.800 1.700
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
GXX chi1 N CA CB CG 180.000 15.000 3
GXX chi2 CA CB CG CD 180.000 15.000 3
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
GXX chir_01 CA N CB C negativ
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
GXX plan CD 0.020
GXX plan CG 0.020
GXX plan OE1 0.020
# ------------------------------------------------------
LYX LYX 'LYXINE ' L-peptide
22 9 .
#
data_comp_LYX
#
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
LYX N N NH1 -0.204
LYX H H HNH1 0.204
LYX CA C CH1 0.058
LYX HA H HCH1 0.046
LYX CB C CH2 -0.076
LYX HB1 H HCH2 0.038
LYX HB2 H HCH2 0.038
LYX CG C CH2 -0.076
LYX HG1 H HCH2 0.038
LYX HG2 H HCH2 0.038
LYX CD C CH2 -0.076
LYX HD1 H HCH2 0.038
LYX HD2 H HCH2 0.038
LYX CE C CH2 -0.013
LYX HE1 H HCH2 0.098
LYX HE2 H HCH2 0.098
LYX NZ N NT3 -0.204
LYX HZ1 H HNT3 0.204
LYX C C C 0.318
LYX O O O -0.422
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
LYX N n/a CA START
LYX H N . .
LYX CA N C .
LYX HA CA . .
LYX CB CA CG .
LYX HB1 CB . .
LYX HB2 CB . .
LYX CG CB CD .
LYX HG1 CG . .
LYX HG2 CG . .
LYX CD CG CE .
LYX HD1 CD . .
LYX HD2 CD . .
LYX CE CD NZ .
LYX HE1 CE . .
LYX HE2 CE . .
LYX NZ CE HZ3 .
LYX HZ1 NZ . .
LYX C CA . END
LYX O C . .
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
LYX N H coval 0.860 0.020
LYX N CA coval 1.458 0.019
LYX CA HA coval 0.980 0.020
LYX CA CB coval 1.530 0.020
LYX CB HB1 coval 0.970 0.020
LYX CB HB2 coval 0.970 0.020
LYX CB CG coval 1.520 0.030
LYX CG HG1 coval 0.970 0.020
LYX CG HG2 coval 0.970 0.020
LYX CG CD coval 1.520 0.030
LYX CD HD1 coval 0.970 0.020
LYX CD HD2 coval 0.970 0.020
LYX CD CE coval 1.520 0.030
LYX CE HE1 coval 0.970 0.020
LYX CE HE2 coval 0.970 0.020
LYX CE NZ coval 1.489 0.030
LYX NZ HZ1 coval 0.960 0.020
LYX CA C coval 1.525 0.021
LYX C O coval 1.231 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
LYX H N CA 114.000 3.000
LYX HA CA CB 109.000 3.000
LYX CB CA C 110.100 1.900
LYX HA CA C 109.000 3.000
LYX N CA HA 110.000 3.000
LYX N CA CB 110.500 1.700
LYX HB1 CB HB2 110.000 3.000
LYX HB2 CB CG 108.000 3.000
LYX HB1 CB CG 108.000 3.000
LYX CA CB HB1 109.000 3.000
LYX CA CB HB2 109.000 3.000
LYX CA CB CG 114.100 2.000
LYX HG1 CG HG2 110.000 3.000
LYX HG2 CG CD 108.000 3.000
LYX HG1 CG CD 108.000 3.000
LYX CB CG HG1 109.000 3.000
LYX CB CG HG2 109.000 3.000
LYX CB CG CD 111.300 2.300
LYX HD1 CD HD2 110.000 3.000
LYX HD2 CD CE 108.000 3.000
LYX HD1 CD CE 108.000 3.000
LYX CG CD HD1 109.000 3.000
LYX CG CD HD2 109.000 3.000
LYX CG CD CE 111.300 2.300
LYX HE1 CE HE2 110.000 3.000
LYX HE2 CE NZ 108.000 3.000
LYX HE1 CE NZ 108.000 3.000
LYX CD CE HE1 109.000 3.000
LYX CD CE HE2 109.000 3.000
LYX CD CE NZ 111.900 3.200
LYX CE NZ HZ1 110.000 3.000
LYX N CA C 111.200 2.800
LYX CA C O 120.800 1.700
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
LYX chi1 N CA CB CG 180.000 15.000 3
LYX chi2 CA CB CG CD 180.000 15.000 3
LYX chi3 CB CG CD CE 180.000 15.000 3
LYX chi4 CG CD CE NZ 180.000 15.000 3
LYX hh CD CE NZ HZ1 60.000 30.000 3
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
LYX chir_01 CA N CB C negativ
# ------------------------------------------------------
# --- LIST OF LINKS ---
#
data_link_list
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
XLINK GXX . . LYX . .
AMIDE-XLINK
data_link_XLINK
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
XLINK 1 CD 2 NZ single 1.329 0.014
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
XLINK 1 OE1 1 CD 2 NZ 123.000 1.600
XLINK 1 CG 1 CD 2 NZ 116.200 2.000
XLINK 1 CD 2 NZ 2 HZ1 124.300 3.000
XLINK 1 CD 2 NZ 2 CE 121.700 1.800
loop_
_chem_link_tor.link_id
_chem_link_tor.id
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
XLINK psi 1 CB 1 CG 1 CD 2 NZ 160.00 30.0 2
XLINK omega 1 CG 1 CD 2 NZ 2 CE 180.00 5.0 0
XLINK phi 1 CD 2 NA 2 CE 2 CD 60.00 20.0 3
loop_
_chem_link_plane.link_id
_chem_link_plane.plane_id
_chem_link_plane.atom_comp_id
_chem_link_plane.atom_id
_chem_link_plane.dist_esd
XLINK plane1 1 CG 0.020
XLINK plane1 1 CD 0.020
XLINK plane1 1 OE1 0.020
XLINK plane1 2 NZ 0.020
XLINK plane2 1 CD 0.020
XLINK plane2 2 NZ 0.020
XLINK plane2 2 CE 0.020
XLINK plane2 2 HZ1 0.020
#
