Demo Prepare

Run it by typing MMMx demo_Prepare. This example generates logfile demo_Prepare.log.

Modules used

Only module Prepare is used.

Source code

% MMMx Demo: Preparation of the structure of ABC-transporter BtuCD in complex
%            with its periplasmic binding protein BtuF for further modelling
%            structures 2QI9 and 5M29 (cobinamide-bound BtuF) are processed
%            - non-standard residues MSE are replaced by the wild-type MET
%            - coordinates are centered
%            - coordinates are transformed into a pseudo-symmetry frame
%            - lipid-bilayer geometry is optimized, leading to another frame
%              transformation
%            - cobinamide-bound BtuF is superimposed onto BtuF of the entire
%              transporter and a chimera is generated

# log 


   getpdb 2ADC NMR
   save rb34 NMR RB34 {3}(A)334-528
   getpdb 2QI9 BtuCDF % load BtuCDF as template

   center (A,B) BtuCDF

   symmetry backbone BtuCDF % only backbone coordinates are used for pseudo-symmetry transform

   save BtuCDF_centered BtuCDF

   deselenate BtuCDF % replaces selenium amino acids (for phasing x-ray data) by sulfur counterparts

   save BtuCDF_deselenated BtuCDF

   bilayer bundle oriented BtuCDF % determine bilayer thickness and center protein in lipid bilayer

   save BtuCDF_bilayer_transform BtuCDF 2QI9 % save template structure after transformation

   getpdb 5M29 BtuF_CBI % load BtuD with cobinamide bound

   chains (A) BtuF_CBI % only chain A of 5M29 is used

   remove (A)302 BtuF_CBI % remove cyanide ion and glycerol molecules  
   remove (A)303 BtuF_CBI
   remove (A)304 BtuF_CBI

   save BtuF_CBI_removal BtuF_CBI

   superimpose BtuF_CBI.(A) BtuCDF.(F) align backbone % superimpose [2M29](A) onto [2QI9](F)

   replace BtuCDF.(F) BtuF_CBI.(A) % replace chain F in [2QI9] by chain A of [2M29]

   save BtuCDF_chimera BtuCDF BTUX % save chimera generated by the replacement

   renumber (F) -20 BtuCDF

   save BtuCDF_chimera_renumbered BtuCDF BTUX % save chimera generated by the replacement


# report


The first example loads the ensemble structure 2ADC from the PDB into entity NMR. Then it saves a local PDB file rb34.pdb that contains only residues 334-528 of chain A in only model 3 of the ensemble.

The second example generates a chimera from two structures related to vitamin B12 transporter BtuCDF in a frame related to a lipid bilayer and renumbers one of the chains.

First, the PDB file 2QI9 is downloaded as initial model with internal name BtuCDF. Then the coodinates are translated, so that chains A and B (the transmembrane part) are centered. A pseudo-symmetry axis is computed that relates chains A and B and the coordinates are transformed so that this pseudo-symmetry axis is the z axis. This model is saved as file BtuCDF_centered.pdb.

Then, selenium amino acids, which were used for phasing the x-ray data, are replaced by their (native) sulfur counterparts. This model is saved as file BtuCDF_deselenated.pdb.

Now, a bilayer geometry is computed in helix bundle mode, assuming that the z axis (here the pseudo-symmetry axis) is the bilayer normal (mode oriented). This model is saved as file BtuCDF_bilayer_transform.pdb. Compared to the previous model, only the z coordinates have changed, so that z = 0 corresponds to the bilayer central plane. The optimal bilayer thickness and the applied coordinate shift are rported in the logfile.

Then, PDB file 5M29 is downlaoded as internal entity BtuF_CBI. This structure is the substrate-binding protein BtuF in complex with cobinamid. The structure contains a cyanide ion and two glycerol molecules that are not required in the chimera. They are removed in the following. This model is saved as file BtuF_CBI_removal.pdb.

The substrate-binding protein, which is chain A in 2M29 is superimposed on the substrate-binding protein in BtuCDF, where it is chain F. Directive align uses sequence alignment to match residue numbers. Directive backbone superimposes backbone atoms.

Chain F in model BtuCDF is then replaced by chain A in model BtuF_CBI. Because the cofactor cobinamide is a cofactor of chain A of this model, this introduces the substrate molecule into the chimera. The chimera is saved to file BtuCDF_chimera with pseudo-PDB code BTUX.

The final part demonstrates renumbering of chain F, with all new residue numbers decreased by 20. This models is saved to file BtuCDF_chimera_renumbered.pdb.


All outputs, except for the logfile, are PDB files. All intermediate models are stored here. In most application scenarios, it will be sufficient to save the final model.