T4 Lysozyme (M6I)
CELL 72.200 73.800 150.500 90.00 90.00 90.00 INCLUDE /usr/local/tnt/data/symmetry/p212121.dat FO r-free/1m06i_exp.hkl RESOLUTION 2.2 INCLUDE ../../t4l.seq RENAME CHAIN_TYPE NULL TO T4L CHANGE RESIDUE_TYPE OF T4L|6 TO ILE CHAIN A T4L CHAIN B T4L CHAIN C T4L CHAIN D T4L ASSUME RESIDUE_TYPE HOH WHEN_CONTAINS OH CLUSTER NTERM RESIDUE 11 - 59 CHAINS A B C D CLUSTER CTERM RESIDUE 1 - 10 RESIDUE 60 - 162 CHAINS A B C D COMBINE XYZ A|11 - 59 COMBINE XYZ A|1 - 10 A|60 - 162 COMBINE XYZ B|11 - 59 COMBINE XYZ B|1 - 10 B|60 - 162 COMBINE XYZ C|11 - 59 COMBINE XYZ C|1 - 10 C|60 - 162 COMBINE XYZ D|11 - 59 COMBINE XYZ D|1 - 10 D|60 - 162 CONSTANT B CONSTANT OCC WEIGHT RFACTOR 0.0005 WEIGHT BOND 0.8 ANGLE 1.3 TORSION 0 WEIGHT TRIGONAL 2 PLANE 5 CONTACT 0 BCORREL 1.0
This is the control file which performs rigid-body refinement on the model of the T4 lysozyme mutant M6I. There are four molecules in the asymmetric unit, each with differing angles between the N and C terminal domains. Each of the eight domains is refined as a distinct group. The interesting part is that the first ten amino acids move with the C terminal domain, not the expected N terminal domain. The CLUSTER statements define the ncs which permits the use of the ncs command to monitor the similarity of the various domains. The COMBINE statements create the rigid bodies.
To prevent the, possibly, incorrect location of the surface loops of the molecule from causing the domains to be misplaced, the weight for bad contacts has been set to zero.
Note the way the sequence of this mutant is defined. First the sequence file the the wild type enzyme is read. Since this sequence is defined in terms of the ``chain with no name" the chain type is renamed to be clearer. Then the residue type of residue number 6 is changed to reflect the mutation. Each chain is defined to have the resulting sequence.
The advantage of this scheme is that the sequence of the majority of the protein does not have to be recreated for each mutant. In addition, it is very clear from looking at the control file that the only mutation in this protein is at residue 6. Often T4 lysozyme mutants are made in a non-wild type background and it can be confusing if this is forgotten.