2LP6

Refined Solution NMR Structure of the 50S ribosomal protein L35Ae from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target (NESG) PfR48

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	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
2	2D 1H-13C HSQC aliphatic	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
3	2D 1H-13C HSQC aromatic	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
4	3D HNCO	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
5	3D CBCA(CO)NH	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
6	3D HNCACB	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
7	3D HBHA(CO)NH	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
8	3D CCC(CO)NH TOCSY	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
9	3D HCCH-TOCSY	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
10	3D HCCH-COSY	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
11	3D HNHA	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
12	3D 1H-15N NOESY	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
13	3D 1H-13C NOESY aliphatic	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	100% D2O		6.5	ambient	293
14	3D 1H-13C NOESY aromatic	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
15	3D 1H-13C NOESY aliphatic	1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293
16	2D 1H-13C HSQC high resolution	0.29 mM [U-5% 13C; U-100% 15N] PfR48.002, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	750
3	Varian	INOVA	800

NMR Refinement
Method	Details	Software
simulated annealing	THE FINAL REFINED STRUCTURES ARE BASED ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (18.3 CONSTRAINTS PER RESIDUE, 7.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 91 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 1.3) 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 BY GEL FILTRATION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN, FOLLOWED BY MANUAL SIDE CHAIN ASSIGNMENT. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus, AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING THE C-TERMINAL HIS6): BACKBONE, 98.2%, SIDE CHAIN, 90.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 84.2%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 91, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,21-76,79-87: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.0. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 97.0%, ADDITIONALLY ALLOWED, 3.0%, DISALLOWED, 0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.56/-1.89, ALL, -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.13/-1.07 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 91): RECALL, 0.965, PRECISION, 0.878, F-MEASURE, 0.920, DP-SCORE, 0.784. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 5. THE FINAL FOUR UNASSIGNED HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG 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]: 1,13-20,77-78,88-91.

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	data analysis	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
6	data analysis	AutoAssign	1.9	Zimmerman, Moseley, Kulikowski and Montelione
7	chemical shift assignment	AutoAssign	1.9	Zimmerman, Moseley, Kulikowski and Montelione
8	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
9	collection	VNMR	6.1B	Varian
10	data analysis	Sparky	3	Goddard
11	structure solution	TALOS+		Shen, Cornilescu, Delaglio and Bax
12	data analysis	PSVS	1.4	Bhattacharya, Montelione
13	data analysis	PdbStat	5.5	Tejero, Montelione
14	data analysis	MolProbity	3.19	Richardson