2KT1

Solution NMR Structure of the SH3 Domain from the p85beta subunit of Phosphatidylinositol 3-kinase from H.sapiens, Northeast Structural Genomics Consortium Target HR5531E

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
2	2D 1H-13C HSQC	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
3	3D 1H-15N NOESY	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
4	3D 1H-13C NOESY aliphatic	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
5	3D 1H-13C NOESY aromatic	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
6	3D 1H-13C arom NOESY	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
7	3D HNCO	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
8	3D HN(CA)CO	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
9	3D CBCA(CO)NH	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
10	3D HNCACB	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
11	3D HBHA(CO)NH	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
12	3D HBHANH	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
13	3D HCCH-COSY	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
14	3D HCCH-TOCSY	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
15	3D CCH-TOCSY	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
16	3D HNCA	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
17	1D 1H-15N T1 and T2	0.62 mM [U-100% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
18	2D 1H-13C HSQC high res. (L/V methyl stereoassignment)	0.50 mM [U-5% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308
19	2D 1H-15N hetNOE	0.50 mM [U-5% 13C; U-100% 15N] HR5531E, 20 mM sodium phosphate, 100 mM sodium chloride, 50 uM DSS, 10 mM DTT	95% H2O/5% D2O		6.5	ambient	308

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800
2	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
simulated annealing, null	THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 972 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 108 DIHEDRAL ANGLE CONSTRAINTS (13.5 CONSTRAINTS PER RESIDUE, 5.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 82 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19.	CNS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Additional NMR Experimental Information

Details

THE PROTEIN IS PREDOMINANTLY MONOMERIC AT 308 K BY 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CRYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 94.5%, SIDE CHAIN, 89.5%, AROMATICS, 86.8%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 80.0%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE NUMBERS 1 TO 82, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 7-16,18-81: (A) RMSD (ORDERED RESIDUES): BB, 0.7, HEAVY ATOM, 1.3. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.8%, ADDITIONALLY ALLOWED, 8.1%, GENEROUSLY ALLOWED, 0.1%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.44/-1.42, ALL, -0.32/-1.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 17.41/-1.46 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-82): RECALL, 0.969, PRECISION, 0.904, F-MEASURE, 0.935, DP-SCORE, 0.797. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 7. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
2	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
3	rpf analysis	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
4	chemical shift assignment	PINE	1.0	Bahrami, Markley, Assadi, and Eghbalnia
5	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6	data analysis	Sparky	3.112	Goddard
7	peak picking	Sparky	3.112	Goddard
8	collection	TopSpin	2.1	Bruker Biospin
9	data analysis	TopSpin	2.1	Bruker Biospin
10	structure quality analysis	PSVS	1.4	Bhattacharya and Montelione
11	dihedral angle constraints	TALOS	plus	Cornilescu, Delaglio and Bax
12	pdb coordinate analysis	PdbStat	5.1	Tejero and Montelione