2LOY

Refined Miminal Constraint Solution NMR Structure of Translationally-controlled tumor protein (TCTP) from Caenorhabditis elegans, Northeast Structural Genomics Consortium Target WR73

SOLUTION NMR

---

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
2	2D 1H-15N TROSY-HSQC	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
3	2D 1H-13C HSQC aliphatic	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
4	3D HNCO	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
5	3D HN(CA)CO	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
6	3D TROSY-HNCACB	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
7	3D TROSY-HN(CO)CACB	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
8	3D 1H-15N NOESY	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
9	3D 1H-13C NOESY aliphatic	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
10	3D 15N-15N-1H NOESY	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
11	3D 13C-13C-1H NOESY	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
12	3D 15N-13C-1H NOESY	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
13	3D 13C-15N-1H NOESY	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
14	3D C(CO)NH TOCSY	0.822 mM [U-100% 13C; U-100% 15N; U-100% 2H; ILVFY-1H] WR73.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
15	2D 1H-13C HSQC high resolution	0.85 mM [U-5% 13C; U-100% 15N] WR73.004, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
16	NH J-MODULATION (RDC)	0.6 mM [U-5% 13C; U-100% 15N] WR73.011, 11.55 mg/ml Pf1 phage, 12 mM MES, 400 mM NaCl, 6 mM DTT, 3 mM Cacl2	90% H2O/10% D2O		6.5	ambient	298

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

NMR Refinement
Method	Details	Software
simulated annealing	THE FINAL RDC-REFINED MINIMAL CONSTRAINT STRUCTURES ARE BASED ON A TOTAL OF 970 CONFORMATIONALLY-RESTRICTING DISTANCE CONSTRAINTS, 293 DIHEDRAL ANGLE CONSTRAINTS, 126 HYDROGEN BOND CONSTRAINTS, and 99 N-H RESIDUAL DIPOLAR COUPLINGS FROM A SINGLE ALIGNMENT IN PHAGE. (7.7 CONSTRAINTS PER RESIDUE, 2.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 183 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 FINAL 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 MONOMERIC AT 298 K BY 15N T1/T2 RELAXATION AND STATIC LIGHT SCATTERING. THE STRUCTURE IS A MINIMAL CONSTRAINT STRUCTURE DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CRYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN METHYL ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE NUMBERS 1 TO 183, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,18-38,66-106,111-146,152-162,164-181: (A) RMSD (ORDERED RESIDUES): BB, 1.0, HEAVY ATOM, 1.6. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 96.8%, ALLOWED, 2.9%, DISALLOWED, 0.2%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.28/-0.79, ALL, -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.30/-1.10 (E) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 40. (F) AGREEMENT WITH N-H RESIDUAL DIPOLAR COUPLINGS: CORRELATION COEFFICIENT (R): 0.985; Qrms: 0.171. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1,13-17,39-65,107-110,147-151,163,182-183.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.3	Brunger, Adams, Clore, Gros, Nilges and Read
2	structure solution	CNS	1.3	Brunger, Adams, Clore, Gros, Nilges and Read
3	geometry optimization	CNS	1.3	Brunger, Adams, Clore, Gros, Nilges and Read
4	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
5	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6	data collection	TopSpin	2.1	Bruker Biospin
7	data collection	VnmrJ		Varian
8	chemical shift assignment	PINE	1.0	Bahrami, Markley, Assadi, and Eghbalnia
9	data analysis	Sparky	3	Goddard
10	peak picking	Sparky	3	Goddard
11	dihedral angle constraints	TALOS+		Shen, Cornilescu, Delaglio and Bax
12	rdc analysis	PALES		PALES (Zweckstetter, Bax)
13	structure validation	PSVS	1.4	Bhattacharya, Montelione
14	quality assessment	PSVS	1.4	Bhattacharya, Montelione
15	data analysis	PdbStat	5.5	Tejero, Montelione
16	structure validation	MolProbity	3.19	Richardson
17	quality assessment	MolProbity	3.19	Richardson