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NMR Solution Structure of a Thiamine Biosynthesis Protein from Geobacter Metallireducens: Northeast Structural Genomics Consortium Target GmR137
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D 1H-15N HSQC
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
2
2D 1H-13C HSQC
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
3
(4,3)D GFT-HNNCABCA
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
4
(4,3)D GFT-CABCA(CO)NHN
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
5
(4,3)D GFT-HABCAB(CO)NHN
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
6
3D CBCA(CO)NH
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
7
3D HBHA(CO)NH
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
8
3D HNCO
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
9
3D HCCH-TOCSY
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
10
3D-CCH-TOCSY
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
11
3D 1H-15N NOESY
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
12
3D 1H-13C aliph NOESY
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
13
3D 1H-13C arom NOESY
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
14
3D HCCH-COSY
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
15
2D 1H-15N HSQC
1.26 mM [U-10% 13C; U-99% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
16
2D 1H-15N HSQC
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
17
2D 1H-13C HSQC
1.06 mM [U-100% 13C; U-100% 15N] GmR137, THiS protein
90% H2O/10% D2O
5 mM CaCl2, 100mM NaCl
6.5
ambient
293
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
800
2
Varian
INOVA
600
3
Varian
INOVA
500
NMR Refinement
Method
Details
Software
simulated annealing
The structure was obtained using triple resonance NMR spectroscopy. GFT-NMR experiments were used for backbone resonance assignments and conventional 3D TOCSY and COSY experiments were used to obtain sidechain resonance assignments. Automated NOESY assignments were made using AUTOSTRUCTURE and CYANA-2.1. Dihedral angle constraints were obtained from TALOS. The structure calculation was done excluding 5 HIS from 8-residue C-terminal tag (LEHHHHHH). Completeness of assignments excluding 5-HIS: Backbone - 100%, Sidechain (aliphatic) - 99% Sidechain (aromatic) - 96%. The assignments were validated using AVS software. Final structure quality factros (excluding 5 HIS) determined using PSVS-v1.3: Ordered residues are defiend as: 1-13, 18-29, 32-63. (a) RMSD (ordered residues) all backbone atoms: 0.7A and heavy atoms: 1.2A. (b) Ramachandran statistics for ordered residues: Most favored region: 82.8%, additionally allowed regions: 17.0% generously allowed region: 0.1%, disallowed regions: 0.1%. (c) Procheck scores for ordered residues (RAW/Z-): Phi/psi -0.58/-1.97, all -0.48/-2.84, (d) MolProbity clashscores (RAW/Z-) 17.03/-1.40, (e) RPF scores for the goodness of the fit to NOESY data: Recall - 0.99, Precision - 0.942, F-measure - 0.966 and final dp score - 0.88. (f) Number of close contacts for 20 models: 6, RMS deviation for bond angles - 0.6deg, RMS deviation for bond lengths - 0.009A.