1OO9 | pdb_00001oo9

Orientation in Solution of MMP-3 Catalytic Domain and N-TIMP-1 from Residual Dipolar Couplings

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	15N-separated NOESY; HNCA; HNCO; HN(CO)CA	0.8mM MMP-3 U-15N, 13C; 0.8mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O	93% H2O/7% D2O	20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide	6.6	ambient	310
2	HCCH-TOCSY; HCCH-COSY;	0.8mM MMP-3 U-15N, 13C; 0.8mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O	93% H2O/7% D2O	20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide	6.6	ambient	310
3	15N-separated NOESY; HNCA; HNCO; HN(CO)CA	0.66mM N-TIMP-1 U-15N, 13C; 0.66mM MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O	93% H2O/7% D2O	20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide	6.7	ambient	307
4	15N-separated NOESY	0.3mM 98% 2H/15N N-TIMP-1; 0.3mM MMP-3 (E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O	93% H2O/7% D2O	20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide	6.7	ambient	307
5	15N-separated NOESY	0.5mM MMP-3 U-2H, 15N; 0.5mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O	93% H2O/7% D2O	20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide	6.6	ambient	310
6	15N-separated NOESY	0.3mM 98% 2H/15N N-TIMP-1; 0.3mM (15N-IV, 15N, 13C-L)MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O	93% H2O/7% D2O	20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide	6.7	ambient	307
7	coupled 15N-HSQC; coupled 13C-HSQC; Ha-coupled HNCA	0.3mM 98% 2H/15N N-TIMP-1; 0.3mM (15N-IV, 15N, 13C-L)MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O 5% PEG(C12E6)/1-hexanol	93% H2O; 7% D2O 5% PEG(C12E6)/1-hexanol	20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide	6.7	ambient	307

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	500
2	Varian	UNITYPLUS	720
3	Bruker	DRX	750
4	Varian	INOVA	600

NMR Refinement
Method	Details	Software
RIGID BODY MINIMIZATION FOLLOWED BY RESTRAINED SIMULATED ANNEALING	STRUCTURES WERE CALCULATED USING XPLOR-NIH. REFINEMENTS WERE CARRIED OUT FIRST BY RIGID BODY MINIMIZATION (CLORE(2000) PROC.NATL.ACAD.SCI. 97, 9021-9025) FOLLOWED BY RESTRAINED SIMULATED ANNEALING (WANG ET AL. EMBO J. (2000) 19,5635-5649). THE CRYSTAL STRUCTURE OF THE COMPLEX BY BODE ET AL. (NATURE (1997), 389, 77-81; PDB CODE: 1UEA) HAS BEEN USED AS A STARTING POINT WITH PROTONS ATTACHED AND TAKING ONLY N-TERMINAL 126 RESIDUES OF TIMP-1. INTERFACIAL SIDE CHAINS OF THE FOLLOWING RESIDUES WERE ALLOWED TO BE FLEXIBLE: CHAIN A (MMP-3(DC)): 162-169,198-202, 205-206, 211 AND 221-223; CHAIN B (N-TIMP-1): 302-304, 329, 333-335,366-369; A TOTAL OF 49 NOE (46 INTERMOLECULAR AND 3 INTRAMOLECULAR) 75 NH DIPOLAR COULINGS FOR N-TIMP-1, 19 NH DIPOLAR COUPLINGS AND 8 CaHa DIPOLAR COUPLINGS FOR MMP-3 WERE USED FOR REFINEMENT. TARGET FUNCTIONS INCLUDE TERMS FOR NOE RESTRAINTS, DIPOLAR COUPLING RESTRAINTS AND RADIUS OF GYRATION. ALSO, MODULE ( DOSSET ET AL. J. BIOMOL. NMR, (2001),20,223-231) AND PALES (ZWECKSTETTER AND BAX, J. AM. CHEM. SOC (2000), 122, 3791-3792) WERE USED FOR EVALUATING THE ORIENTATION AND STRUCTURES.	XPLOR

NMR Ensemble Information
Conformer Selection Criteria	lowest energy structure
Conformers Calculated Total Number	25
Conformers Submitted Total Number	1

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	XPLOR	NIH	BRUNGER
2	data analysis	PALES	SGI Irix 6.2	ZWECKSTETTER AND BAX
3	data analysis	Module	1.0	DOSSET ET AL