| CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS | THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302) THE TARGET FUNCTIONS COMPRISES TERMS FOR THE EXPERIMENTAL NOE RESTRAINTS AND SIDECHAIN TORSION ANGLE RESTRAINTS; A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136); A MULTIIMENSIONAL TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE (CLORE & KUSZEWSKI (2002) J.AM.CHEM.SOC. 124, 2866-2867); AND A RADIUS OF GYRATION POTENTIAL (KUSZEWSKI ET AL (1999) J.AM.CHEM.SOC. 121, 2337-2338). THE STARTING COORDINATES OF PHOSPHOIIBMTL ARE TAKEN FROM THE NMR STRUCTURE ((PDB ACCESSION CODE 1VRV, SUH ET AL. (2005) J.MOL.BIOL. 353, 1129-1136). THE STARTING STRUCTURE FOR IIAMTL IS TAKEN FROM THE COORDINATES OF IIAMTL IN THE IIAMTL-HPR COMPLEX (PDB ACCESSION CODE 1J6T; CORNILESCU ET AL. (2002) J.BIOL.CHEM. 277,42289-42298). THE COORDINATES OF IIAMTL IN THIS COMPLEX ARE DERIVED FROM MOLECULE D OF THE 1.8A RESOLUTION CRYSTAL STRUCTURE OF IIAMTL PDB ACCESSION CODE 1A3A, VAN MONTFORT ET AL. STRUCTURE 5, 217-225 (1998)). IN THE STRUCTURE DETERMINATION OF THE IIAMTL-PHOSPHOIIBMTL COMPLEX, THE BACKBONE COORDINATES AND NON-INTERFACIAL SIDECHAINS ARE TREATED AS RIGID BODIES THROUGHOUT WITH IIAMTL HELD FIXED AND PHOSPHOIIBMTL ALLOWED TO ROTATE AND TRANSLATE. THE INTERFACIAL SIDECHAINS ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM.
IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS
DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING
STRUCTURES (TOTAL OF 200) AND THE MEAN COORDINATE POSITIONS. IT
IS IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE
ATOMS AND NON-INTERFACIAL SIDECHAINS PROVIDE ONLY A
MEASURE OF THE PRECISION WITH WHICH THE RELATIVE
OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES
NOT TAKE INTO ACCOUNT THE ERRORS IN THE NMR COORDINATES
OF PHOSPHOIIBMTL AND THE XRAY/NMR COORDINATES OF IIAMTL.
THE COORDINATES DEPOSITED CORRESPOND TO THE RESTRAINED
REGULARIZED MEAN COORDINATES. THE STRUCTURE IS BASED ON
84 INTERMOLECULAR NOE RESTRAINTS BETWEEN IIAMTL AND IIBMTL;
37 INTRAMOLECULAR NOE RESTRAINTS FOR IIAMTL AND 46
46 INTRAMOLECULAR NOE RESTRAINTS FOR IIBMTL RELATED
ONLY TO INTERFACIAL SIDECHAINS; AND 55 SIDECHAIN TORSION ANGLE
RESTRAINTS (36 FOR IIAMTL AND 19 FOR IIBMTL) RELATED
TO INTERFACIAL SIDECHAINS ONLY.
DEVIATIONS FROM NOE DISTANCE RESTRAINTS: 0.009 A
DEVIATIONS FROM SIDECHAIN TORSION ANGLE RESTRAINTS: 0.31 DEG
DEVIATIONS FROM IDEALIZED GEOMETRY: BONDS 0.006A,
ANGLES: 0.9 DEG, IMPROPER TORSIONS 1.3 DEG. | Xplor-NIH |
