histo-blood group antigens
I want to add a trisaccharide to my structure, but when I run phenix.refine the sugar breaks up. I know I need to specify the links on the sugar and that they must be in the reverse order, but I don't know how to do that. i.e., Some thing like this... which worked fine with a different sugar (below) refinement.pdb_interpretation { apply_cif_link { data_link = ALPHA1-2 residue_selection_1 = chain D and resname GAL and resid 2 residue_selection_2 = chain D and resname FUC and resid 1 } apply_cif_link { data_link = BETA1-3 residue_selection_1 = chain D and resname NGA and resid 3 residue_selection_2 = chain D and resname GAL and resid 2 BUT now I have a new sugar (below is the pdb). I want to create the links, does anyone know how to do this? HETATM 2386 C1 FUC A 1 16.834 10.319 -8.554 1.00 66.42 C HETATM 2387 C2 FUC A 1 16.606 11.012 -7.166 1.00 61.84 C HETATM 2388 C3 FUC A 1 17.009 12.513 -7.241 1.00 59.45 C HETATM 2389 C4 FUC A 1 16.144 13.200 -8.308 1.00 60.73 C HETATM 2390 C5 FUC A 1 16.343 12.478 -9.659 1.00 61.11 C HETATM 2391 C6 FUC A 1 15.451 13.074 -10.752 1.00 58.85 C HETATM 2392 O1 FUC A 1 18.293 10.173 -8.848 1.00 75.63 O HETATM 2393 O2 FUC A 1 17.360 10.357 -6.166 1.00 60.01 O HETATM 2394 O3 FUC A 1 16.815 13.162 -5.990 1.00 59.75 O HETATM 2395 O4 FUC A 1 14.774 13.159 -7.919 1.00 58.98 O HETATM 2396 O5 FUC A 1 16.051 11.063 -9.520 1.00 61.98 O HETATM 2397 C1 GAL A 2 18.717 9.760 -11.037 1.00 85.92 C HETATM 2398 C2 GAL A 2 18.373 9.162 -9.615 1.00 83.98 C HETATM 2399 C3 GAL A 2 19.592 8.289 -9.187 1.00 87.51 C HETATM 2400 C4 GAL A 2 19.814 7.192 -10.269 1.00 87.23 C HETATM 2401 C5 GAL A 2 20.123 7.872 -11.635 1.00 86.28 C HETATM 2402 C6 GAL A 2 20.336 6.876 -12.795 1.00 83.95 C HETATM 2403 O2 GAL A 2 17.629 10.430 -11.635 1.00 91.09 O HETATM 2404 O3 GAL A 2 18.638 6.383 -10.380 1.00 88.24 O HETATM 2405 O4 GAL A 2 19.031 8.744 -12.000 1.00 86.74 O HETATM 2406 O5 GAL A 2 20.641 7.401 -14.059 1.00 79.17 O HETATM 2407 O6 GAL A 2 20.370 8.579 -8.053 1.00 95.12 O HETATM 2408 C1 NGA A 3 20.960 9.184 -6.913 1.00100.54 C HETATM 2409 C2 NGA A 3 20.707 8.446 -5.548 1.00103.23 C HETATM 2410 C3 NGA A 3 20.064 9.437 -4.546 1.00103.55 C HETATM 2411 C4 NGA A 3 21.015 10.661 -4.359 1.00103.72 C HETATM 2412 C5 NGA A 3 21.252 11.342 -5.751 1.00103.24 C HETATM 2413 C6 NGA A 3 22.221 12.560 -5.693 1.00103.28 C HETATM 2414 C7 NGA A 3 20.349 6.053 -6.269 1.00107.39 C HETATM 2415 C8 NGA A 3 19.294 4.961 -6.441 1.00107.38 C HETATM 2416 N2 NGA A 3 19.860 7.256 -5.781 1.00105.47 N HETATM 2417 O3 NGA A 3 19.829 8.805 -3.291 1.00102.40 O HETATM 2418 O4 NGA A 3 22.255 10.230 -3.783 1.00105.38 O HETATM 2419 O5 NGA A 3 21.766 10.375 -6.714 1.00101.87 O HETATM 2420 O6 NGA A 3 22.993 12.697 -6.878 1.00104.86 O HETATM 2421 O7 NGA A 3 21.514 5.860 -6.552 1.00110.32 O END Kindly, Grant
Hansman, Grant (NIH/VRC) [F] wrote:
I want to add a trisaccharide to my structure, but when I run phenix.refine the sugar breaks up. I know I need to specify the links on the sugar and that they must be in the reverse order, but I don’t know how to do that.
i.e., Some thing like this… which worked fine with a different sugar (below) . .
BUT now I have a new sugar (below is the pdb). I want to create the links, does anyone know how to do this?
Maybe refine.geometry_restraints.edits {} Find the following in .eff or .def and edit: geometry_restraints.edits { excessive_bond_distance_limit = 10 bond { action = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None distance_ideal = None sigma = None slack = None } . . } (duplicate the bond{} as needed) atom selection syntax: atom_selection_1 = chain D and resname CYS and resid 101 and name SG atom_selection_2 = chain D and resname HEC and resid 4003 and name CAB
HETATM 2386 C1 FUC A 1 16.834 10.319 -8.554 1.00 66.42 C
HETATM 2387 C2 FUC A 1 16.606 11.012 -7.166 1.00 61.84 C
HETATM 2388 C3 FUC A 1 17.009 12.513 -7.241 1.00 59.45 C
HETATM 2389 C4 FUC A 1 16.144 13.200 -8.308 1.00 60.73 C
HETATM 2390 C5 FUC A 1 16.343 12.478 -9.659 1.00 61.11 C
HETATM 2391 C6 FUC A 1 15.451 13.074 -10.752 1.00 58.85 C
HETATM 2392 O1 FUC A 1 18.293 10.173 -8.848 1.00 75.63 O
HETATM 2393 O2 FUC A 1 17.360 10.357 -6.166 1.00 60.01 O
HETATM 2394 O3 FUC A 1 16.815 13.162 -5.990 1.00 59.75 O
HETATM 2395 O4 FUC A 1 14.774 13.159 -7.919 1.00 58.98 O
HETATM 2396 O5 FUC A 1 16.051 11.063 -9.520 1.00 61.98 O
HETATM 2397 C1 GAL A 2 18.717 9.760 -11.037 1.00 85.92 C
HETATM 2398 C2 GAL A 2 18.373 9.162 -9.615 1.00 83.98 C
HETATM 2399 C3 GAL A 2 19.592 8.289 -9.187 1.00 87.51 C
HETATM 2400 C4 GAL A 2 19.814 7.192 -10.269 1.00 87.23 C
HETATM 2401 C5 GAL A 2 20.123 7.872 -11.635 1.00 86.28 C
HETATM 2402 C6 GAL A 2 20.336 6.876 -12.795 1.00 83.95 C
HETATM 2403 O2 GAL A 2 17.629 10.430 -11.635 1.00 91.09 O
HETATM 2404 O3 GAL A 2 18.638 6.383 -10.380 1.00 88.24 O
HETATM 2405 O4 GAL A 2 19.031 8.744 -12.000 1.00 86.74 O
HETATM 2406 O5 GAL A 2 20.641 7.401 -14.059 1.00 79.17 O
HETATM 2407 O6 GAL A 2 20.370 8.579 -8.053 1.00 95.12 O
HETATM 2408 C1 NGA A 3 20.960 9.184 -6.913 1.00100.54 C
HETATM 2409 C2 NGA A 3 20.707 8.446 -5.548 1.00103.23 C
HETATM 2410 C3 NGA A 3 20.064 9.437 -4.546 1.00103.55 C
HETATM 2411 C4 NGA A 3 21.015 10.661 -4.359 1.00103.72 C
HETATM 2412 C5 NGA A 3 21.252 11.342 -5.751 1.00103.24 C
HETATM 2413 C6 NGA A 3 22.221 12.560 -5.693 1.00103.28 C
HETATM 2414 C7 NGA A 3 20.349 6.053 -6.269 1.00107.39 C
HETATM 2415 C8 NGA A 3 19.294 4.961 -6.441 1.00107.38 C
HETATM 2416 N2 NGA A 3 19.860 7.256 -5.781 1.00105.47 N
HETATM 2417 O3 NGA A 3 19.829 8.805 -3.291 1.00102.40 O
HETATM 2418 O4 NGA A 3 22.255 10.230 -3.783 1.00105.38 O
HETATM 2419 O5 NGA A 3 21.766 10.375 -6.714 1.00101.87 O
HETATM 2420 O6 NGA A 3 22.993 12.697 -6.878 1.00104.86 O
HETATM 2421 O7 NGA A 3 21.514 5.860 -6.552 1.00110.32 O
END
Kindly,
Grant
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One note about FUC. Is the Fucose you want alpha-L? (Your pdb has alpha-L) I would make sure what is in the dictionary file is alpha (it wasn't a while ago, it might have been fixed now). Moreover, the ALPHA1-2 link works correctly only for D sugars. The work around is to use the wrong linkage (BETA1-2) to get it right for a-L-fucose. Type this to find the file that describes how the linkages are defined: phenix.where_mon_lib_list_cif And you need two more "}"s to close the block, which you probably already know. In an ALPHA1-2 linkage, the residue_selection_1 is the residue that links at C2, and residue_selection_2 is the residue that links at C1. For BETA1-3, first residue is the one that links at C3, and the second residue is the one that links at C1. Try this: (I am not sure if I understand your structure, your NGA has a planar C1 centre. I thought NGA is supposed to have an sp3-hybridized carbon there, you can check HIC-UP. I am going to assume you intended a beta anomer for NGA) refinement.pdb_interpretation { apply_cif_link { data_link = BETA1-2 residue_selection_1 = chain D and resname GAL and resid 2 residue_selection_2 = chain D and resname FUC and resid 1 } apply_cif_link { data_link = BETA1-3 residue_selection_1 = chain D and resname GAL and resid 2 residue_selection_2 = chain D and resname NAG and resid 3 } } You also need to provide phenix a monomer library file for NGA, I don't think there is a full description in the phenix monomer library (maybe there is now in 1.6.1). Go to the HIC-UP page for NGA (Go to QuickXS, under QuickXS II, type NGA), from that page go to the PRODRG2 webpage (using the Go button under Description), and copy the refmac description into a file like NGA.cif. Then use this in your refinement. Good luck, Engin On 4/20/10 4:14 PM, Hansman, Grant (NIH/VRC) [F] wrote:
I want to add a trisaccharide to my structure, but when I run phenix.refine the sugar breaks up. I know I need to specify the links on the sugar and that they must be in the reverse order, but I don’t know how to do that.
i.e., Some thing like this… which worked fine with a different sugar (below)
refinement.pdb_interpretation {
apply_cif_link {
data_link = ALPHA1-2
residue_selection_1 = chain D and resname GAL and resid 2
residue_selection_2 = chain D and resname FUC and resid 1
}
apply_cif_link {
data_link = BETA1-3
residue_selection_1 = chain D and resname NGA and resid 3
residue_selection_2 = chain D and resname GAL and resid 2
BUT now I have a new sugar (below is the pdb). I want to create the links, does anyone know how to do this?
HETATM 2386 C1 FUC A 1 16.834 10.319 -8.554 1.00 66.42 C
HETATM 2387 C2 FUC A 1 16.606 11.012 -7.166 1.00 61.84 C
HETATM 2388 C3 FUC A 1 17.009 12.513 -7.241 1.00 59.45 C
HETATM 2389 C4 FUC A 1 16.144 13.200 -8.308 1.00 60.73 C
HETATM 2390 C5 FUC A 1 16.343 12.478 -9.659 1.00 61.11 C
HETATM 2391 C6 FUC A 1 15.451 13.074 -10.752 1.00 58.85 C
HETATM 2392 O1 FUC A 1 18.293 10.173 -8.848 1.00 75.63 O
HETATM 2393 O2 FUC A 1 17.360 10.357 -6.166 1.00 60.01 O
HETATM 2394 O3 FUC A 1 16.815 13.162 -5.990 1.00 59.75 O
HETATM 2395 O4 FUC A 1 14.774 13.159 -7.919 1.00 58.98 O
HETATM 2396 O5 FUC A 1 16.051 11.063 -9.520 1.00 61.98 O
HETATM 2397 C1 GAL A 2 18.717 9.760 -11.037 1.00 85.92 C
HETATM 2398 C2 GAL A 2 18.373 9.162 -9.615 1.00 83.98 C
HETATM 2399 C3 GAL A 2 19.592 8.289 -9.187 1.00 87.51 C
HETATM 2400 C4 GAL A 2 19.814 7.192 -10.269 1.00 87.23 C
HETATM 2401 C5 GAL A 2 20.123 7.872 -11.635 1.00 86.28 C
HETATM 2402 C6 GAL A 2 20.336 6.876 -12.795 1.00 83.95 C
HETATM 2403 O2 GAL A 2 17.629 10.430 -11.635 1.00 91.09 O
HETATM 2404 O3 GAL A 2 18.638 6.383 -10.380 1.00 88.24 O
HETATM 2405 O4 GAL A 2 19.031 8.744 -12.000 1.00 86.74 O
HETATM 2406 O5 GAL A 2 20.641 7.401 -14.059 1.00 79.17 O
HETATM 2407 O6 GAL A 2 20.370 8.579 -8.053 1.00 95.12 O
HETATM 2408 C1 NGA A 3 20.960 9.184 -6.913 1.00100.54 C
HETATM 2409 C2 NGA A 3 20.707 8.446 -5.548 1.00103.23 C
HETATM 2410 C3 NGA A 3 20.064 9.437 -4.546 1.00103.55 C
HETATM 2411 C4 NGA A 3 21.015 10.661 -4.359 1.00103.72 C
HETATM 2412 C5 NGA A 3 21.252 11.342 -5.751 1.00103.24 C
HETATM 2413 C6 NGA A 3 22.221 12.560 -5.693 1.00103.28 C
HETATM 2414 C7 NGA A 3 20.349 6.053 -6.269 1.00107.39 C
HETATM 2415 C8 NGA A 3 19.294 4.961 -6.441 1.00107.38 C
HETATM 2416 N2 NGA A 3 19.860 7.256 -5.781 1.00105.47 N
HETATM 2417 O3 NGA A 3 19.829 8.805 -3.291 1.00102.40 O
HETATM 2418 O4 NGA A 3 22.255 10.230 -3.783 1.00105.38 O
HETATM 2419 O5 NGA A 3 21.766 10.375 -6.714 1.00101.87 O
HETATM 2420 O6 NGA A 3 22.993 12.697 -6.878 1.00104.86 O
HETATM 2421 O7 NGA A 3 21.514 5.860 -6.552 1.00110.32 O
END
Kindly,
Grant
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-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
participants (3)
-
Edward A. Berry -
Engin Ozkan -
Hansman, Grant (NIH/VRC) [F]