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