PDB Files

The files 1bcc.pdb and 3bcc.pdb in this directory are the coordinate files submitted to the Brookhaven Protein Database in March 98 as updates for entries 1bcc and 3bcc.

 

File 1bcc

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:

.SPACE_GROUP_operators 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 it's 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):

.SPACE_GROUP_OPERATORS 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

 

File 3bcc

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:

.SPACE_GROUP_operators 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 it's 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):

.SPACE_GROUP_OPERATORS 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 transform 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

 

File 1bccdimref.pdb

This file contains the coordinated for the complete dimer of the native complex.

 

File 3bccdimref.pdb

This file contains the coordinated for the complete dimer of the complex containing stigmatellin and antimycin.

 

File 1bcc_m.pdb

This file contains the coordinated for the three catalytic subunits of the "functional monomer" of the native complex, abstracted from the file 1bccdimref.pdb.

 

File 3bcc_m.pdb

This file contains the coordinated for the three catalytic subunits of the "functional monomer" of the complex containing stigmatellin and antimycin, abstracted from the file 3bccdimref.pdb.