2JRF
Solution NMR structure of Tubulin polymerization-promoting protein family member 3 from Homo sapiens. Northeast Structural Genomics target HR387.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 2 | 2D 1H-13C HSQC | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 3 | 3D 1H-15N NOESY | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 4 | 3D 1H-13C NOESY | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 5 | 3D 1H-13C NOESY aromatic | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 6 | 3D HNCO | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 7 | 3D HN(CA)CO | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 8 | 3D HN(COCA)CB | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 9 | 3D HNCACB | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 10 | 3D C(CO)NH-TOCSY | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 11 | 3D CCH-TOCSY | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 12 | 3D CCH-TOCSY aromatic | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 13 | 3D HCCH-COSY | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 14 | 3D HNHA | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 15 | 3D HCCH-TOCSY | 1.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| 16 | 2D 1H-13C HSQC high res. | 0.7 mM [U-5% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide | 95% H2O/5% D2O | 100 mM | 5.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | THE STRUCTURES ARE BASED ON A TOTAL OF 1554 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 120 DIHEDRAL ANGLE CONSTRAINTS, AND 74 HYDROGEN BOND CONSTRAINTS (11.4 CONSTRAINTS PER RESIDUE, 2.6 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 178 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). | TopSpin |
| 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 STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 98.1%, SIDE CHAIN, 88.3%, AROMATICS, 91.8%, STEREOSPECIFIC METHYL, 65.0%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 178, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 9-19,23-24,28-45,53-62,69-86,92-103: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 95.0%, ADDITIONALLY ALLOWED, 5.0%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.26/1.34, ALL, 0.18/1.06. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 12.78/-0.67. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-178): RECALL, 0.972, PRECISION, 0.878, F-MEASURE, 0.922, DP-SCORE, 0.726. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI) + S(PSI) < 1.8): 1-8,20-22,25-27,46-52,63-68,87-91,104-178 |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | 1.3 | Bruker Biospin |
| 2 | chemical shift assignment | AutoAssign | 2.4.0 | Zimmerman, Moseley, Kulikowski and Montelione |
| 3 | peak picking | Sparky | 3.110 | Goddard |
| 4 | data analysis | Sparky | 3.110 | Goddard |
| 5 | structure solution | AutoStructure | 2.1.1 | Huang, Tejero, Powers and Montelione |
| 6 | processing | NMRPipe | 2.3 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 7 | structure solution | X-PLOR NIH | 2.11.2 | Schwieters, Kuszewski, Tjandra and Clore |
| 8 | refinement | X-PLOR NIH | 2.11.2 | Schwieters, Kuszewski, Tjandra and Clore |
| 9 | refinement | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 10 | data analysis | PSVS | 1.3 | Bhattacharya and Montelione |
| 11 | structure validation | PSVS | 1.3 | Bhattacharya and Montelione |
| 12 | pdb analysis | PdbStat | 5.0 | Tejero and Montelione |
| 13 | dihedral angle constraints | TALOS | Cornilescu, Delaglio and Bax | |
