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
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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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 | |
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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 | |
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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 | ||||
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# | 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 |