[ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes

2013-05-21 Thread 孙庆祥
hi all,


Sorry if this has been asked before. I wonder if there is an list or library of 
most commonly co-crystallized ligands(or solvent molecules) available? Better 
if the electron density maps of the ligands are also shown with different 
resolutions. That could help a lot for an inexperienced crystallographer (like 
me) to quickly identify extra electron densities in a new structure, by simply 
comparing the electron density shapes. 


I remember a few days ago somebody asked about a PEG electron density, which 
looks like a string of beads. If I knew that earlier, I could have modeled it 
in, instead of waters...


Thanks,
Jeremy 

Re: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes

2013-05-21 Thread Das, Debanu
Hi Jeremy,

Given the large number of different kinds of ligands that are observed (either 
from crystallization, purification conditions or endogenous), I think it will 
be really difficult to assign just by visual and manual comparison with a 
standard set, especially for inexperienced crystallographers.

Better to use modules like LigandFit in Phenix, which can use the Refmac ligand 
library or user-defined library to scan the putative ligand density in 
difference maps in the structure.

If you want a nice overview of different common ligands that have been observed 
in ~3000 structures from PSI/Structural Genomics efforts (including a whole 
bunch of unidentified ligands), along with their PDB ids so you can see 
corresponding density, have  a look at this paper:

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1309-16. 
doi: 10.1107/S1744309110008092. Epub 2010 Jul 6.
Ligands in PSI structures.
Kumar A, Chiu HJ, Axelrod HL, Morse A, Elsliger MA, Wilson IA, Deacon A.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator 
Laboratory, Menlo Park, CA, USA.
PMID: 20944227
http://www.ncbi.nlm.nih.gov/pubmed/20944227

Best,
Debanu.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
Sent: Tuesday, May 21, 2013 12:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] list/library of most commonly co-crystallized 
ligands/solvents and/or their electron density shapes

hi all,

Sorry if this has been asked before. I wonder if there is an list or library of 
most commonly co-crystallized ligands(or solvent molecules) available? Better 
if the electron density maps of the ligands are also shown with different 
resolutions. That could help a lot for an inexperienced crystallographer (like 
me) to quickly identify extra electron densities in a new structure, by simply 
comparing the electron density shapes. 


I remember a few days ago somebody asked about a PEG electron density, which 
looks like a string of beads. If I knew that earlier, I could have modeled it 
in, instead of waters...

Thanks,
Jeremy 




Re: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes

2013-05-21 Thread Jeffrey, Philip D.
Top 20 HETNAM entries based on 58,469 PDB entries at better than 2.5 Angstrom 
resolution (arbitrary cut):

Number of entries in histogram: 14864
Total number of instances : 195481

   0 14502 0.0742 GOL(glycerol)
   1 10952 0.0560 SO4
   2  8064 0.0413  ZN
   3  7628 0.0390  MG
   4  6930 0.0355 MSE (SeMet)
   5  6685 0.0342  CA
   6  6555 0.0335 EDO (Ethylene glycol)
   7  6315 0.0323  CL
   8  5856 0.0300 HEM
   9  3922 0.0201  NA
  10  3647 0.0187 NAG
  11  3148 0.0161 PO4
  12  2360 0.0121 ACT(Acetate)
  13  1874 0.0096  MN
  14  1561 0.0080 NAP
  15  1387 0.0071   K
  16  1338 0.0068 FAD
  17  1277 0.0065 PLP (PYRIDOXAL-5'-PHOSPHATE)
  18  1228 0.0063 TRS(Tris buffer)
  19  1205 0.0062 FMN

(numeric columns are ranking; count; frequency)
No electron density, sorry.
Clearly I should be adding more glycerols.

Phil Jeffrey
Princeton

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 孙庆祥 
[baby_ten...@163.com]
Sent: Tuesday, May 21, 2013 3:29 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] list/library of most commonly co-crystallized 
ligands/solvents and/or their electron density shapes

hi all,

Sorry if this has been asked before. I wonder if there is an list or library of 
most commonly co-crystallized ligands(or solvent molecules) available? Better 
if the electron density maps of the ligands are also shown with different 
resolutions. That could help a lot for an inexperienced crystallographer (like 
me) to quickly identify extra electron densities in a new structure, by simply 
comparing the electron density shapes.

I remember a few days ago somebody asked about a PEG electron density, which 
looks like a string of beads. If I knew that earlier, I could have modeled it 
in, instead of waters...

Thanks,
Jeremy




Re: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes

2013-05-21 Thread Katherine Sippel
I'm not sure that a library of ligand electron density would be an entirely
good thing. I guess something small like an acetate or DMSO would be
relatively consistent but larger things like PEGS or even glycerols are
going to be dependent on the nature of the binding site. A good example
would be to look at something that binds ATP as an enzymatic co-factor
versus a binding protein. Completely different geometry.

For a beginner I'd suggest to always check your difference peaks and all
your waters between rounds of refinement. If the positive density peaks are
covalent bond distance apart, it's not a water. If you've got giant green
smears between or around your waters it might not be a water. If you've
got good enough density and can guess at a basic framework you can plug a
rough sketch into the chemical structure search function in PubChem that
can give you some possible options. You can cross-reference the hits to the
HIC-Up server or the PDB for restraints or density examples keeping in mind
that your ligand-protein interactions may be different. Also do a sanity
check and ask yourself does this make chemical sense? If you've modeled
something in there is TWILIGHT to see if your density supports your model.
Of course there is also experimental evidence but that's a different can of
worms. Basically really look at your data and if something seems hinky then
look for alternatives.

My $0.02,
Katherine




On Tue, May 21, 2013 at 3:05 PM, Jeffrey, Philip D.
pjeff...@princeton.eduwrote:

  Top 20 HETNAM entries based on 58,469 PDB entries at better than 2.5
 Angstrom resolution (arbitrary cut):

  Number of entries in histogram: 14864
 Total number of instances : 195481

 0 14502 0.0742 GOL(glycerol)
1 10952 0.0560 SO4
2  8064 0.0413  ZN
3  7628 0.0390  MG
4  6930 0.0355 MSE (SeMet)
5  6685 0.0342  CA
6  6555 0.0335 EDO (Ethylene glycol)
7  6315 0.0323  CL
8  5856 0.0300 HEM
9  3922 0.0201  NA
   10  3647 0.0187 NAG
   11  3148 0.0161 PO4
   12  2360 0.0121 ACT(Acetate)
   13  1874 0.0096  MN
   14  1561 0.0080 NAP
   15  1387 0.0071   K
   16  1338 0.0068 FAD
   17  1277 0.0065 PLP (PYRIDOXAL-5'-PHOSPHATE)
   18  1228 0.0063 TRS(Tris buffer)
   19  1205 0.0062 FMN

  (numeric columns are ranking; count; frequency)
 No electron density, sorry.
   Clearly I should be adding more glycerols.

  Phil Jeffrey
 Princeton

   *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 孙庆祥 [
 baby_ten...@163.com]
 *Sent:* Tuesday, May 21, 2013 3:29 PM
 *To:* CCP4BB@JISCMAIL.AC.UK
 *Subject:* [ccp4bb] list/library of most commonly co-crystallized
 ligands/solvents and/or their electron density shapes

   hi all,

  Sorry if this has been asked before. I wonder if there is an list or
 library of most commonly co-crystallized ligands(or solvent molecules)
 available? Better if the electron density maps of the ligands are also
 shown with different resolutions. That could help a lot for an
 inexperienced crystallographer (like me) to quickly identify extra electron
 densities in a new structure, by simply comparing the electron density
 shapes.

  I remember a few days ago somebody asked about a PEG electron density,
 which looks like a string of beads. If I knew that earlier, I could have
 modeled it in, instead of waters...

  Thanks,
 Jeremy