Experiment: 2L3F

Solution NMR Structure of a putative Uracil DNA glycosylase from Methanosarcina acetivorans, Northeast Structural Genomics Consortium Target MvR76

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
2	2D 1H-13C HSQC	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
3	3D 1H-15N NOESY	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
4	3D 1H-13C NOESY aliphatic	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
5	3D 1H-13C NOESY aromatic	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
6	2D 1H-13C HSQC high resolution (L/V methyl stereoassignment)	1.15 mM [U-5% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
7	3D HNCO	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
8	3D HN(CA)CO	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
9	3D HNCA	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
10	3D HN(CO)CA	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
11	3D CBCA(CO)NH	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
12	3D HNCACB	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
13	3D HBHA(CO)NH	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
14	3D HCCH-TOCSY	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
15	3D CCH-TOCSY	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
16	3D HCCH-COSY	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
17	3D HNHA	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
18	3D HBHANH	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
19	1D 15N T1 and T2	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
20	2D 1H-15N hetNOE	0.94 mM [U-100% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
21	NH J-modulation	0.80 mM [U-5% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 4 % C12E5 PEG	90% H2O/10% D2O		6.5	ambient	298
22	NH J-modulation	1.15 mM [U-5% 13C; U-100% 15N] MvR76, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 7 % Polyacrylamide gel	90% H2O/10% D2O		6.5	ambient	298

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

NMR Refinement
Method	Details	Software
simulated annealing	THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2729 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 234 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (18.4 CONSTRAINTS PER RESIDUE, 5.4 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 161 BY PSVS 1.4). IN ADDITION, 210 RESOLVED N-H RESIDUAL DIPOLAR COUPLINGS FOR ORDERED RESIDUES OBTAINED FROM TWO ALIGNMENTS WERE INCLUDED IN ALL STRUCTURE CALCULATIONS. 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
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, STATIC LIGHT SCATTERING AND 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 CROYOPROBE. 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 His5): BACKBONE, 98.5%, SIDE CHAIN, 91.0%, AROMATICS, 84.3%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 64.0%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 161, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-34,39-81,92-144,146-160: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 89.1%, ADDITIONALLY ALLOWED, 10.8%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.26/-0.71, ALL, -0.15/-0.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 16.95/-1.38 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 161): RECALL, 0.951, PRECISION, 0.899, F-MEASURE, 0.924, DP-SCORE, 0.722. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 11. THE FINAL FIVE HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION.

Additional NMR Experimental Information

Details

THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 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 CROYOPROBE. 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 His5): BACKBONE, 98.5%, SIDE CHAIN, 91.0%, AROMATICS, 84.3%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 64.0%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 161, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-34,39-81,92-144,146-160: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 89.1%, ADDITIONALLY ALLOWED, 10.8%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.26/-0.71, ALL, -0.15/-0.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 16.95/-1.38 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 161): RECALL, 0.951, PRECISION, 0.899, F-MEASURE, 0.924, DP-SCORE, 0.722. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 11. THE FINAL FIVE HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
2	refinement	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
3	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
4	rpf analysis	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
5	structure quality analysis	PSVS	1.4	Bhattacharya and Montelione
6	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
7	structure quality analysis	MolProbity	3.18	Richardson
8	collection	TopSpin	2.1	Bruker Biospin
9	data analysis	TopSpin	2.1	Bruker Biospin
10	pdb coordinate analysis	PdbStat	5.1	Tejero & Montelione
11	chemical shift assignment	PINE	1.0	Bahrami, Markley, Assadi, and Eghbalnia
12	data analysis	Sparky	3.112	Goddard
13	peak picking	Sparky	3.112	Goddard
14	geometry optimization	TALOS+		Shen, Cornilescu, Delaglio and Bax
15	rdc analysis	PALES		PALES (Zweckstetter, Bax)
16	collection	VnmrJ	2.1	Varian
17	data analysis	VnmrJ	2.1	Varian

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

2L3F | pdb_00002l3f

Solution NMR Structure of a putative Uracil DNA glycosylase from Methanosarcina acetivorans, Northeast Structural Genomics Consortium Target MvR76