I am forwarding an answer I sent previously in response
to a similar question. We used refmac5 to refine a number of acyl-enzyme
structures:
Radisky ES, Lee JM, Lu CJ, Koshland DE Jr.
Insights
into the serine protease mechanism from atomic resolution structures
of
trypsin reaction intermediates.
Proc Natl Acad Sci U S A. 2006 May
2;103(18):6835-40.
We kept distance restraints loose and did not use angle
restraints on the acyl-enzyme linkage, in order that it should refine with
heavier weight on the experimental data.
Cheers,
Evette
Evette S. Radisky,
Ph.D.
Assistant
Professor and Associate Consultant II
Mayo Clinic Cancer Center
Griffin Cancer Research Building, Rm
310
4500 San Pablo
Road
Jacksonville, FL
32224
(904) 953-6372
(office)
(904)
953-3109
(lab)
I just checked some of my files where I created an acyl
link like that - as I recall, it took some fiddling (and help from others at the
ccp4bb) to get the formatting right. Here is what worked in my
pdb:
LINK
C ARG A
5
OG SER X
195
ARG-SER
Plus,
you then have to define the link in a .cif library file that is also
supplied to refmac; mine looked like this:
[note,
I was purposefully using a very loose restraint on the bond length; a more
typical restraint (if you really think you know what the distance is supposed to
be) would be 0.02 instead of 0.2]
global_
_lib_name
?
_lib_version
?
_lib_update ?
#
------------------------------------------------
# --- 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
ARG-SER ARG .
.
SER
.
.
bond_ARG-C_=_SER-OG
#
------------------------------------------------------
#
# --- DESCRIPTION
OF LINKS
---
#
data_link_ARG-SER
#
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
ARG-SER 1 C 2 OG
coval
1.330 0.200
#
------------------------------------------------------
Good luck!
Evette
Evette S. Radisky, Ph.D.
Assistant Professor and Associate
Consultant II
Mayo Clinic Cancer Center
Griffin Cancer Research Building, Rm
310
4500 San Pablo Road
Jacksonville, FL 32224
(904) 953-6372 (office)
(904) 953-2857 (lab)
Dear all,
I encountered some difficulties to define a link between the C-terminal
residue of a protein with an other covalently-bound protein for refinement under
Refmac. I tried to define it as a LINK command in the header of the PDB, but it
seems that it is not refined at all...
Here is what is present in my header:
LINK
OG SER A 85
1.330 C GLY B
276
SER-GLY
What did I do wrong? Could any body help me? Should I specify
something more in the script file?
Thanks a lot in advance.
Leo
PS: sorry if the question has already been answered...
==========================
Chavas Leonard M.G.,
Ph.D.
Structural Research
Center
KEK,PF. 1-1
Oho
Tuskuba, Ibaraki -
Japan
---------------------------------------------
PHS: +81(0)29-864-5200 (ext:
2682)
==========================