3SAK

HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAC STRUCTURES)


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D AND 4D TRIPLE AND DOUBLE RESONANCE HETERONUCLEAR EXPERIMENTS 308
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAMX600 AND DMX600600
NMR Refinement
MethodDetailsSoftware
simulated annealingTERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS 3JHNALPHA COUPLING CONSTANT RESTRAINTS (GARRETT ET AL J. MAGN. RESON. B104, 99-103 (1994). TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI J, GRONENB CLORE, GM J AM CHEM SOC 121, 2337-2338 (1999)) TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI J, GRONEN CLORE GM. PROTEIN SCI 5, 1067-1080 (1996); J. MAGN 125, 171-177 (1997). COVALENT GEOMETRY RESTRAINTS (BONDS, ANGLES, IMPROPER QUARTIC VAN DER WAALS REPULSION TERM (NILGES. M, GRONENBORN, A.M., BRUNGER, A.T., CLORE, G.M. (1988) PROTEIN ENG. 2, 27-38). THE 3D STRUCTURE OF THE OLIGOMERIZATION DOMAIN (RESIDUES 319 - 360) OF P53 BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 4472 EXPERIMENTAL RESTRAINTS COMPRISING THE FOLLOWING INTRA- AND INTER-SUBUNIT RESTRAINTS: (A) INTRASUBUNIT: 852 SEQUENTIAL (|I-J|=1), 712 MEDIUM RANGE (1 < |I-J| >=5) AND 76 LONG RANGE (|I-J| >5) INTERRESIDUES AND 740 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 136 DISTANCE RESTRAINTS FOR 68 HYDROGEN BONDS, 284 TORSION ANGLE (144 PHI, 104 CHI1, AND 36 CHI2) RESTRAINTS, AND 144 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS. (B) INTERSUBUNIT: 244 A-B/C-D, 876 A-C/B-D, 40 A-D/B-C APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 40 DISTANCE RESTRAINTS FOR 20 HYDROGEN BONDS INVOLVING THE A-C/B-D SUBUNITS, AND 36 DISTANCE RESTRAINTS FOR 4 WATER MOLECULES. IN ADDITION, THERE ARE A TOTAL OF 38 CALPHA AND 35 CB CHEMICAL SHIFT RESTRAINTS PER SUBUNIT THAT HAVE BEEN INCORPORATED INTO THE REFINEMENT [J. KUSZWESKI, J. QIN, A.M. GRONENBORN AND G.M. CLORE, J. MAGN RESON. SER B 106, 92-96 (1995)]. THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT. 229, 317-324. ALL STRUCTURAL STATISTICS ARE GIVEN IN THE SOURCE REFERENCE. THIS ENTRY CONTAINS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE, FOLLOWED BY THE 22 INDIVIDUAL SIMULATED ANNEALING STRUCTURES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAI BY FIRST AVERAGING COORDINATES OF THE INDIVIDUAL 22 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 326 - 354 OF ALL FOUR SUBUNITS, AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 OF THE RESTRAINED MINIMIZED MEA STRUCTURE (THE B-FACTOR COLUMN IN X-RAY STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE NUMBERS IN COLUMNS 61 - 66 OF THE INDIVIDUAL STRUCTURES HAVE NO MEANING. NOTE THAT RESIDUES 319 - 323 AT THE N-TERMINUS AND RESIDUES 357 - 360 AT THE C-TERMINUS ARE COMPLETELY DISORDERED. TERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING: NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS 3JHNALPHA COUPLING CONSTANT RESTRAINTS (GARRETT ET AL J. MAGN. RESON. B104, 99-103 (1994). TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI J, GRONENB CLORE, GM J AM CHEM SOC 121, 2337-2338 (1999)) TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI J, GRONEN CLORE GM. PROTEIN SCI 5, 1067-1080 (1996); J. MAGN 125, 171-177 (1997). COVALENT GEOMETRY RESTRAINTS (BONDS, ANGLES, IMPROPER QUARTIC VAN DER WAALS REPULSION TERM (NILGES. M, GRONENBORN, A.M., BRUNGER, A.T., CLORE, G.M. (1988) PROTEIN ENG. 2, 27-38). THE 3D STRUCTURE OF THE OLIGOMERIZATION DOMAIN (RESIDUES 319 - 360) OF P53 BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 4472 EXPERIMENTAL RESTRAINTS COMPRISING THE FOLLOWING INTRA- AND INTER-SUBUNIT RESTRAINTS: (A) INTRASUBUNIT: 852 SEQUENTIAL (|I-J|=1), 712 MEDIUM RANGE (1 < |I-J| >=5) AND 76 LONG RANGE (|I-J| >5) INTERRESIDUES AND 740 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 136 DISTANCE RESTRAINTS FOR 68 HYDROGEN BONDS, 284 TORSION ANGLE (144 PHI, 104 CHI1, AND 36 CHI2) RESTRAINTS, AND 144 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS. (B) INTERSUBUNIT: 244 A-B/C-D, 876 A-C/B-D, 40 A-D/B-C APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 40 DISTANCE RESTRAINTS FOR 20 HYDROGEN BONDS INVOLVING THE A-C/B-D SUBUNITS, AND 36 DISTANCE RESTRAINTS FOR 4 WATER MOLECULES. IN ADDITION, THERE ARE A TOTAL OF 38 CALPHA AND 35 CB CHEMICAL SHIFT RESTRAINTS PER SUBUNIT THAT HAVE BEEN INCORPORATED INTO THE REFINEMENT [J. KUSZWESKI, J. QIN, A.M. GRONENBORN AND G.M. CLORE, J. MAGN RESON. SER B 106, 92-96 (1995)]. THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT. 229, 317-324. ALL STRUCTURAL STATISTICS ARE GIVEN IN THE SOURCE REFERENCE. THIS ENTRY CONTAINS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE, FOLLOWED BY THE 22 INDIVIDUAL SIMULATED ANNEALING STRUCTURES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAI BY FIRST AVERAGING COORDINATES OF THE INDIVIDUAL 22 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 326 - 354 OF ALL FOUR SUBUNITS, AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 OF THE RESTRAINED MINIMIZED MEA STRUCTURE (THE B-FACTOR COLUMN IN X-RAY STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE NUMBERS IN COLUMNS 61 - 66 OF THE INDIVIDUAL STRUCTURES HAVE NO MEANING. NOTE THAT RESIDUES 319 - 323 AT THE N-TERMINUS AND RESIDUES 357 - 360 AT THE C-TERMINUS ARE COMPLETELY DISORDERED.XPLOR/CNS
NMR Ensemble Information
Conformer Selection CriteriaSIMULATED ANNEALING
Conformers Calculated Total Number23
Conformers Submitted Total Number23
Representative Model1 (restrained minimized mean structure)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementXPLOR/CNSBRUNGER, A., CLORE, G.M. ET AL.
2structure solutionXPLOR/CNSBRUNGER, A., CLORE, G.M. ET AL.