2K53
NMR solution structure of A3DK08 protein from Clostridium thermocellum: Northeast Structural Genomics Consortium Target CmR9
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 | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
2 | 2D 1H-15N HSQC | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
3 | 2D 1H-13C HSQC | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
4 | 2D 1H-13C HSQC | 1.05 mM [U-10% 13C; U-99% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
5 | 3D CBCA(CO)NH | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
6 | 3D HNCACB | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
7 | 3D HNCO | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
8 | 3D HBHA(CO)NH | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
9 | 3D HCCH-TOCSY | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
10 | 3D 1H-13C NOESY | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
11 | 3D 1H-15N NOESY | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
12 | 3D 1H-13C NOESY | 0.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | The structure was determined using triple resonance NMR spectroscopy. Automated backbone resonance assignments were made using AUTOASSIGN and the sidechain assignments were completed manually. Automated NOESY assignments were made using AUTOSTRUCTURE and CYANA-2.1. Dihedral angle constraints were obtained from TALOS. The structure calculations were done excluding the six HIS from the 8-residue C-terminal tag(LEHHHHHH). Completeness of assignments excluding the HHHHHH: Backbone:100% Sidechain(aliphatic): 99% Sidechain (Aromatic): 90% Stereospecific Methyl assignments:100%. The assignments were validated using AVS software. Final structure quality factors(excluding the HHHHHH) determined using PSVS-v1.3: Ordered residues are defined as residues 2-28,33-34,37-69.(a) RMSD (ordered residues)all backbone atoms:0.4A, all heavy atoms: 0.7A; RMSD (all residues) backbone: 0.7A and heavy atoms: 1.0A. (b) Ramachandran statistics for ordered residues : Most favoured regions: 97.1%, additionally allowed regions: 2.9%.(C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI,0.21/1.14, ALL,0.24/1.42 (D) MOLPROBITY CLASH SCORE (RAW/Z-): 17.26/-1.44. (E) RPF scores for the goodness of the fit to NOESY data: Recall:0.984, PRECISION: 0.848, F-measure: 0.911 and final DP-score:0.743. (f) Number of close contacts for 20 models: 6. RMS deviation for bond angles:0.6deg. RMS deviation for bond lengths 0.008A. | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
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 | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
3 | chemical shift assignment | AutoAssign | 2.4.0 | Zimmerman, Moseley, Kulikowski and Montelione |
4 | noesy assignments | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |