Re: [ccp4bb] Refining an acyl-enzyme intermediate

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Refining an acyl-enzyme intermediate
From: Jaeyong_Lee jaeyongl {- at -} SFU {- dot -} CA
Date: 2007-07-16

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Subject: Re: Refining an acyl-enzyme intermediate
From: "Radisky, Evette S {- dot -} Ph {- dot -} D {- dot -} " Radisky {- dot -} Evette {- at -} MAYO {- dot -} EDU
Date: 2007-07-16

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)

________________________________

From: Radisky, Evette S. Ph.D.
Sent: Wednesday, December 06, 2006 10:40 AM
To: CCP4BB
Subject: RE: [ccp4bb]: [ccp4bb] Esterification specification in Refmac5

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)

________________________________

From: owner-ccp4bb@dl.ac.uk [mailto:owner-ccp4bb@dl.ac.uk] On Behalf Of
Leo Chavas
Sent: Wednesday, December 06, 2006 4:21 AM
To: CCP4BB
Cc: Leo Chavas
Subject: [ccp4bb]: [ccp4bb] Esterification specification in Refmac5

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)
e-mail: leo@pfweis.kek.jp
URL: http://pfweis.kek.jp/~leo
==========================

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Refining an acyl-enzyme intermediate
From: Jaeyong_Lee jaeyongl {- at -} SFU {- dot -} CA
Date: 2007-07-16

Next message:
Subject: need help for viewing hardware stereo
From: venkadesan krishnan kvengadesan {- at -} GMAIL {- dot -} COM
Date: 2007-07-16