This directory contains coordinates files (.pdb) specially prepared to facilitate comparing different structures and looking at protein interactions in the dimer which are not present in the monomer. While some of the structures are our own unpublished work, we have also taken files from the PDB. The coordinates were manipulated as follows: 1. Dimerization- where only a monomer was submitted to the PDB, we have generated the dimer using crystallographic or non-crystallo graphic symmetry, as appropriate. 2. Superposition- The structures have been rotated and translated to bring them ito a standard reference position in which the dimer 2-fold axis is along the Z axis, with the N-side toward positive Z. Since the structures are all superposed, they can be compared directly if one's viewer allows loading two molecules, or the same figure can be made from each structure using the same orientation. In this position we estimate that the P-surface of the bilayer hydrophobic zone is at about z=28, and the N surface at z=68. Thus a rough estimate of the fractional way across the dielectric for any given atom at (x,y,z) is given by (z-28)/40 3. Chains have been lettered according to the scheme in use here, with subunits 1-11 labeled A-K in one monomer and N-X in the second. Acknowledgement and disclaimer- The coordiantes for structures solved in other labs were taken from the database and manipulated as described above. All credit for the structures belongs to the depositors, and we take responsibility for any errors introduced. However our responsibility is limited to our sincere apologies and a promise to promptly correct any errors that are brought to our attention. We make no warranty of the suitability of these files for any purpose. The files 1bcc.pdb and 3bcc.pdb in this directory are the coordinate files obtained, after further refinement and error correction, from the same datasets used for the structures 1BCC and 3BCC submitted to the Brookhave Protein Database in March 98. ------------------------------------------------ 1bcc is the structure of the chicken cytochrome bc1 complex from a native crystal. Ubiquinone at the Qi site, two PE molecules, and one OG, are modeled as residues 5, 6, 7, and 8 in chain L. One monomer is presented, the NCS-related monomer can be generated by applying a transform which can be expressed in O datablock form as: .lsq_rt_ncs1bcc r 12 (3f14.7) -0.8350813 -0.5501187 -0.0026849 -0.5501213 0.8350376 0.0089561 -0.0026850 0.0089561 -0.9999563 129.0778355 37.8589104 171.4586645 The structure is presented at its coordinates in its native unit cell. To transform to a reference cell with the dimer 2-fold along the z axis, apply the inverse of the transform (ODB formnat): .lsq_rt_ref21bcc R 12 (3f15.6) 0.018675 0.010478 -0.999771 0.957703 0.287004 0.020898 0.287158 -0.957872 -0.004675 17.905149 174.485565 86.488541 ------------------------------------------------ 3bcc is the structure from a crystal containing stigmatellin and antimycin. Models for these inhibitors are present as residues 5 and 6 of chain L. One monomer is presented, the NCS-related monomer can be generated by applying a transform which can be expressed in O datablock form as: .lsq_rt_ncs3bcc r 12 (3f14.7) -0.8230250 -0.5680065 -0.0002017 -0.5680039 0.8230247 0.0006473 -0.0002021 0.0006488 -0.9999998 129.9098500 40.4159859 170.0044933 The structure is presented at its coordinates in its actual unit cell. To transform to a reference cell with the dimer 2-fold along the z axis, apply the inverse of the transform (ODB formnat): .lsq_rt_ref23bcc R 12 (3f15.6) 0.005187 0.001972 -0.999984 0.954718 0.297463 0.005539 0.297468 -0.954732 -0.000339 17.472937 172.602783 85.056358 ------------------------------------------------ The format of the "O" datablock rotation-translation operators given here is as follows: Lines 2-5 contain the transpose of the rotation matrix Line 6 contains a translation vector to be applied after the rotation. This operator can be used by CCP4 PDBSET program with the syntax: transform [invert] ODB filename.o 1bccref.pdb and 3bccref.pdb are dimers of the same structure, moved to a reference cell in which they should be superimposable. The dimer 2-fold is along the Z axis in this reference cell.