2KKE

Solution NMR Structure of a dimeric protein of unknown function from Methanobacterium thermoautotrophicum, Northeast Structural Genomics Consortium Target TR5

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	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
2	2D 1H-13C HSQC	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
3	3D CBCA(CO)NH	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
4	3D HNCACB	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
5	3D HBHA(CO)NH	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
6	3D HCCH-TOCSY	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
7	3D HNCO	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
8	3D 1H-13C NOESY	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
9	3D 1H-15N NOESY	0.4 mM [U-100% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
10	3D- X-filtered NOESY	0.4 mM [U-10% 13C; U-100% 15N] + unlabeled TR5 protein TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
11	2D 1H-15N HSQC	0.95 mM [U-10% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
12	2D 1H-13C HSQC	0.95 mM [U-10% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303
13	2D HNOE	0.95 mM [U-10% 13C; U-100% 15N] TR5	95% H2O/5% D2O	300 mM NaCl	6.5	1 atm	303

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	UNITY	500

NMR Refinement
Method	Details	Software
simulated annealing	Initial NOESY assignments for the monomer were made using AutoStructure and the solution structure of the dimer was obtained using CYANA-2.1. Constraints for the dimer interface were obtained from the x-filtered NOESY data and slow exchanging amides from H/D exchange. 100 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Initial dihedral angle constraints were obtained from TALOS. Final structure quality factors determined using PSVS software: ordered residues are defined as (10-53,212-236,238-251). (a)RMSD(ordered residues) all Backbone atoms: 0.7A; all heavy atoms: 1.0A. (b) Ramchandran statistics for all ordered residues: Most favoured region: 93.1%; Additionally allowed region: 6.6%; Generously allowed region 0.1% and disallowed region: 0.2%. (c) Procheck scores for all ordered residues (Raw/Z) phi-psi -0.11/-0.12; All: -0.07/-0.41; (d) MolProbity clash score (Raw/Z): 16.97/-1.39. (e) RPF scores for the goodness of fit to NOESY data: Recall :0.913; Precision:0.849; F-measure:0.88; Final DP score :0.703	AutoAssign

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 software. Sidechain assignments were completed manually. The oligomeric state was confirmed to be a dimer from sedimentation-equilibrium analysis (Kd =0.3uM) and static light scattering experiment that reported 90% of the protein in a dimer with a molecular weight of 15.03kD.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	AutoAssign	2.2.1	Zimmerman, Moseley, Kulikowski and Montelione
2	geometry optimization	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
3	geometry optimization	CNS	2.0.6	Brunger, Adams, Clore, Gros, Nilges and Read
4	refinement	CNS	2.0.6	Brunger, Adams, Clore, Gros, Nilges and Read