2K5P
NMR Solution Structure of a Thiamine Biosynthesis Protein from Geobacter Metallireducens: Northeast Structural Genomics Consortium Target GmR137
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Varian | INOVA | 600 |
3 | Varian | INOVA | 500 |
NMR Refinement | ||
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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. | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 140 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | CNS | 2.0.6 | Brunger, Adams, Clore, Gros, Nilges and Read |
2 | structure solution | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
3 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
4 | chemical shift assignment | AutoAssign | 2.4.0 | Zimmerman, Moseley, Kulikowski and Montelione |