2KIM

1.7-mm microcryoprobe solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.

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	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
2	2D 1H-13C HSQC	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
3	3D 1H-13C NOESY aliphatic	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
4	3D 1H-13C NOESY aromatic	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
5	3D HNCO	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
6	3D HN(CA)CO	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
7	3D HNCA	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
8	3D CBCA(CO)NH	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
9	3D HNCACB	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
10	3D HBHA(CO)NH	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
11	3D HCCH-COSY aliphatic	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
12	3D HCCH-TOCSY aliphatic	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
13	3D (H)CCH-TOCSY aliphatic	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
14	3D HNHA	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
15	3D HN(CO)CA	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
16	2D 1H-15N hetNOE	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
17	1D 1H-15N T1 and T2	0.92 mM [U-5% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
18	2D 1H-13C HSQC high res. (L/V methyl stereoassignment)	0.92 mM [U-5% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298
19	3D 1H-15N NOESY	0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	Avance	600

NMR Refinement
Method	Details	Software
simulated annealing	THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1835 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 117 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (19.9 CONSTRAINTS PER RESIDUE, 5.4 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 102 BY PSVS 1.3). 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, AND USING NEUTRAL HISTIDINES (NE2H TAUTOMER) AT POSITIONS 13 and 38.	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 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 AND NOESY SPECTRA USED FOR STRUCTURE CALCULATION WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND 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 TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK AND MOLPROBITY. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.6%, SIDE CHAIN, 98.3%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 102, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 3-32,35-47,51-67,69-100: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 90.6%, ADDITIONALLY ALLOWED, 9.2%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.1%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.13/-0.20, ALL, -0.04/-0.24. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 20.04/-1.91 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-102): RECALL, 0.982, PRECISION, 0.910, F-MEASURE, 0.945, DP-SCORE, 0.788. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 16. (G) MOLPROBITY RAMACHANDRAN ANALYSIS (ALL RESIDUES): 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]: 1-2,33-34,48-50,68,101-102.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TOPSPIN	2.1	Bruker Biospin
2	data analysis	TOPSPIN	2.1	Bruker Biospin
3	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	data analysis	SPARKY	3.112	Goddard
5	peak picking	SPARKY	3.112	Goddard
6	chemical shift assignment	PINE	1.0	Bahrami, Markley, Assadi, and Eghbalnia
7	chemical shift assignment	AutoAssign	2.4.0	Zimmerman, Moseley, Kulikowski and Montelione
8	validation	AutoAssign	2.4.0	Zimmerman, Moseley, Kulikowski and Montelione
9	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
10	refinement	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
11	rpf analysis	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
12	structure quality analysis	PSVS	1.3	Bhattacharya and Montelione
13	structure quality analysis	Molprobity	3.15	Richardson
14	pdb coordinate analysis	PDBstat	5.1	Tejero and Montelione