Student level introduction to autoBUSTER tutorial

Background SULT1A3

Starting Files

sult1a3_tutorial_questions.rtf A question sheet for you to fill in during the exercise
2a3r.mtz the structure factors as supplied by the pdb for 2a3r, converted to mtz format
2a3r.fasta fasta sequence for 2ar3
2a3r.pdb The pdb deposited model for 2a3r, you can use this in the exercise to “cheat” by comparing the current model to– but do not let the actual solution bias your build!
1aqu.pdb estrogen sulfotransferase pdb entry
balbes_molrep_2ar3frame.pdb MR initial model for 2a3r based on 1aqu see below)
balbes -o balbes_out -f 2a3r.mtz -m 1aqu.pdb -s 2a3r.fasta > balbes.log

(A) Using autoBUSTER to calculate an initial map for the SULT1A3 MR model

mkdir sult1a3_tutorial
cd sult1a3_tutorial
(download files here!)
refine -h | more
refine -M list
refine -p balbes_molrep_2ar3frame.pdb -m 2a3r.mtz -d partA -M MapOnly > partA.log &
less partA.log

(B) Using autoBUSTER to do a quick refinement from the SULT1A3 MR model

refine -p balbes_molrep_2ar3frame.pdb \
 -m 2a3r.mtz -d partB -autoncs        \
 -nbig 2 -nsmall 40 > partB.log &
less partB.log
graph_autobuster_R -launch-d partB

(C) Using autoBUSTER to do a long refinement from the SULT1A3 MR model

refine -p balbes_molrep_2ar3frame.pdb \
 -m 2a3r.mtz -d partC -autoncs        \
 -nbig 10 -RB > partC.log &
partC_A27_cf_structures.png partC_A27_cf_init.png partC_A27_cf_final.png
questionA16_coot_new.png questionC6_coot.png

(D) Manually building three residues using coot

In part (C) we looked how autobuster refinement could move the existing incomplete protein model to better explain density. Further progress in improving the model depends making sure it has the correct chemistry corresponding to its sequence. As a learning exercise we will do this for three residues by hand in coot before using an automated tool to correct the whole protein.

refine -p partD_coot_rebuild.pdb \
 -m 2a3r.mtz -d partD -autoncs        \
 -nbig 2 -nsmall 20 > partD.log &

(E) Using coot automated tools to rebuild and refit all the side chains

refine -p partE_coot_rebuild.pdb \
 -m 2a3r.mtz -d partE -autoncs        \
 -nbig 2 > partE.log &

(F) Using coot to clean up the model around 186 HIS

refine -p partF_coot_rebuild.pdb \
 -m 2a3r.mtz -d partF -autoncs        \
 -nbig 2 -nsmall 20 > partF.log &

from here sketch of what needs to be done

(G) Clean up N terminii.

(H) Clean up C terminii.

(I) Clean loop around A 90

(J) Place PAP in A and B chain

(K) build missing helix 65-72

(L) TLS refinement

(M) place dopamine.

Page by Oliver Smart original version 28 May 2008. Updated extensively July 2010, and Feb 2011. Address problems, corrections and clarifications