2JRF | pdb_00002jrf

Solution NMR structure of Tubulin polymerization-promoting protein family member 3 from Homo sapiens. Northeast Structural Genomics target HR387.

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	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