| 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 NOE-DERIVED TERMS FOR THE NOE RESTRAINTS (INTRA AND INTERMOLECULAR), THE INTERFACIAL SIDECHAIN TORSION ANGLE RESTRAINTS FOR IIAGLC, THE BACKBONE AND SIDE CHAIN TORSION ANGLE RESTRAINTS FOR IIBGLC, THE DIPOLAR COUPLING RESTRAINTS FOR IIBGL (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216-221(1998)), THE RADIUS OF GYRATION (KUSZEWSKI ET AL. (1999), A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129- 136), AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE (CLORE & KUSZEWSKI (2002) J.AM.CHEM.SOC 121, 2337-2338). THE STARTING COORDINATES FOR IIAGLC ARE FROM THE 2.1 ANGSTROM RESOLUTION X-RAY STRUCTURE (WITH PROTONS ADDED) OF E. COLI IIAGLC (MOLECULE 2 OF 2F3G; FEESE ET AL. BIOCHEMISTRY 36, 16087-16096 (1997)). THE BACKBONE COORDINATES AND NON- INTERFACIAL SIDECHAINS OF IIAGLC ARE TREATED AS A RIGID BODY.
IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS
DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING
STRUCTURES AND THE MEAN COORDINATE POSITIONS. IT IS
IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE
ATOMS AND NON-INTERFACIAL SIDECHAINS OF IIAGLC
PROVIDE ONLY A MEASURE OF THE PRECISION WITH WHICH THE
RELATIVE ORIENTATION OF IIAGLC IN THE COMPLEX
HAS BEEN DETERMINED AND DOES NOT TAKE INTO ACCOUNT THE
THE ERRORS IN THE X-RAY COORDINATES OF IIAGLC
RESIDUE NUMBERING:
IIAGLC: 19-168 (RESIDUES 1-18 ARE DISORDERED
IN SOLUTION AND NOT VISIBLE IN THE ELECTRON DENSITY
MAP OF THE CRYSTAL STRUCTURE OF THE FREE PROTEIN).
IIBGLC: 314-390 (CORRESPONDING TO RESIDUES 400-476 OF
INTACT IIBCGLC. RESIDUES 301-314 ARE DISORDERED IN
SOLUTION.
PRO317 HAS BEEN MUTATED TO ALA TO REMOVE HETEROGENEITY
ARISING FROM CIS-TRANS PROLINE ISOMERIZATION.
PHOSPHATE: RESIDUE 200
EXPERIMENTAL RESTRAINTS:
INTRAMOLECULAR INTERPROTON DISTANCE RESTRAINTS:
IIBGLC: 987 (189 INTRARESIDUE, 273 SEQUENTIAL,
(218 MEDIUM RANGE (1 < |I-J|<=5,
307 LONG RANGE (|I-J>5)
IIAGLC INTERFACIAL SIDE CHAINS: 30
INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS: 113
BACKBONE H-BOND RESTRAINTS FOR IIBGLC (2 PER H-BOND): 72
TORSION ANGLE RESTRAINTS:
IIBGLC: 221
IIAGLC INTERFACIAL SIDE CHAINS: 34
RESIDUAL DIPOLAR COUPLINGS FOR IIBGLC: 174
(58 N-H, 58 N-C', 58 HN-C')
13CALPHA/BETA SHIFTS FOR IIBGLC: 138
THREE SETS OF COORDINATES ARE GIVEN:
MODEL 3: RESTRAINED REGULARIZED MEAN
COORDINATES OF THE UNPHOSPHORYLATED IIAGLC-IIBGLC COMPLEX
OVERALL BACKBONE COORDINATE PRECISION (IIAGLC+IIBGLC): 0.31A
HEAVY ATOM INTERFACE SIDECHAIN COORDINATE PRECISION
(IIAGLC+IIBGLC): 0.67A
BACKBONE COORDINATE PRECISION FOR IIBGLC: 0.21 A
ALL HEAVY ATOM COORDINATE PRECISION FOR IIBGLC; 0.71 A
MODEL 2: RESTRAINED REGULARIZED MEAN COORDINATES FOR THE
MODEL OF THE DISSOCIATIVE PHOSPHORYL TRANSITION STATE
IIAGLC-IIBGLC. EXPERIMENTAL RESTRAINTS ARE
IDENTICAL TO THOSE USED FOR MODEL 3, BUT COVALENT
GEOMETRY RESTRAINTS ARE INCLUDED RELATING TO THE
PENTACOORDINATE PHOSPHORYL GROUP IN A TRIGONAL BIPYRAMIDAL
GEOMETRY. THE STRUCTURE IS DERIVED FROM
MODEL 3 BY RESTRAINED CONJOINED
TORSION ANGLE/RIGID BODY MINIMIZATION. NO RESTRAINTS
WERE EMPLOYED FOR THE NE2(HIS90/IIAGLC)-P
AND SG(CYS35/IIBGLC)-P DISTANCES. THERE IS NO CHANGE
IN BACKBONE RELATIVE TO MODEL 3 BUT THE NE2(HIS90/IIAGLC-
SG(CYS35/IIBGLC) DISTANCE IS REDUCED FROM 5.75 A IN
MODEL 3 TO 5.3 A IN MODEL 2.
MODEL 1: RESTRAINED REGULARIZED MEAN COORDINATES FOR THE
MODEL OF THE ASSOCIATIVE PHOSPHORYL TRANSITION STATE
HPR-IIAGLC COMPLEX. CALCULATED LIKE MODEL 2 BUT
WITH THE NE2(HIS90/IIAGLC)-P
AND SG(CYS35/IIBGLC)-P DISTANCES RESTRAINED TO 2 A.
THE STRUCTURE IS DERIVED FROM
MODEL 3 BY RESTRAINED CONJOINED
TORSION ANGLE/RIGID BODY MINIMIZATION.
THE RMS DIFFERENCE BETWEEN THE MEAN
STRUCTURES OF THE UNPHOSPHORYLATED COMPLEX (MODEL 3)
AND THE TRANSITION STATE COMPLEX (MODEL 1) IS ONLY 0.1 A
FOR BACKBONE COORDINATES IMMEDIATELY ADJACENT TO THE ACTIVE
SITE HIS AND CYS (RESIDUES 89-91 OF IIAGLC AND
334-336 of IIBGLC). THE REMAINING BACKBONE
COORDINATES DO NOT SHIFT. | X-PLOR NIH |
