CD task7 protocol

Choosing structure

So, we decided to use 2O4H, since it has a bound substrate, low resolution and a listed pH value.

Apo-structure:       2O53 Resolution: 2,7,  R-free: 0,269, pH: 6.0, chains: A,B
Holo-structure:      2O4H Resolution: 2,7,  R-free: 0,271, pH: 6.0, chains: A,B intermediate substrate analog: N-phosphonomethyl-L-aspartate
Apo-structure:       2I3C Resolution: 2,8,  R-free: 0,243, pH: -  , chains: A,B
Ensemble Refinement  2Q51 Resolution: 2,8,  R-free: 0,239, pH: -  , chains: A,B

For 2O4H, there are only missing residues at the N- and C-terminal ends, which can be neglected:

REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) 
REMARK 465   M RES C SSSEQI                                                     
REMARK 465   1 ALA A    -1                                                      
REMARK 465   1 ILE A     0                                                      
REMARK 465   1 ALA A     1                                                      
REMARK 465   1 THR A     2                                                      
REMARK 465   1 SER A     3                                                      
REMARK 465   1 CYS A     4                                                      
REMARK 465   1 HIS A     5                                                      
REMARK 465   1 ILE A     6                                                      
REMARK 465   1 ALA A     7                                                      
REMARK 465   1 GLU A     8                                                      
REMARK 465   1 CYS A   311                                                      
REMARK 465   1 LEU A   312                                                      
REMARK 465   1 HIS A   313

FoldX

list.txt

2O4H.pdb

individual_list.txt

EA285A;
AA305E;
GA123E;
RA71H;
RA71K; 
KA213E;
VA278M;
MA82T;
EA235K;
IA270T;

run.txt

<TITLE>FOLDX_runscript;
<JOBSTART>#;
<PDBS>#;
<BATCH>list.txt;
<COMMANDS>FOLDX_commandfile;
<BuildModel>#,individual_list.txt;
<END>#;
<OPTIONS>FOLDX_optionfile;
<Temperature>298;
<R>#;
<pH>7;
<IonStrength>0.050;
<water>-CRYSTAL;
<metal>-CRYSTAL;
<VdWDesign>2;
<OutPDB>true;
<pdb_hydrogens>false;
<complex_with_DNA> true; 
<END>#;
<JOBEND>#;
<ENDFILE>#;

command

/opt/SS12-Practical/foldx/FoldX.linux64 => choose 3 => run.txt

Minimise

We prepared the .pdb files with pymol (remove hydrogens, solvent)

/opt/SS12-Practical/minimise/minimise E285A_scwrl_repair.pdb E285A_scwrl_min.pdb