2M9U
Solution NMR structure of the C-terminal domain (CTD) of Moloney murine leukemia virus integrase, Northeast Structural Genomics Target OR41A
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 | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
2 | 2D 1H-13C HSQC | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
3 | 3D HNCO | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
4 | 3D CBCA(CO)NH | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
5 | 3D HNCACB | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
6 | 3D HBHA(CO)NH | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
7 | 3D HCCH-TOCSY | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
8 | 3D 13C-edited_NOESY | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
9 | 3D 1H-15N NOESY | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
10 | 3D 13C-edited_NOESY | 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
11 | 2D 1H-15N HSQC | 0.5 mM [U-10% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 | |
12 | 2D 1H-13C HSQC | 0.5 mM [U-10% 13C; U-100% 15N] MLV IN CTD | 90% H2O/10% D2O | 50mM K-glutamate, 100mM NaCl | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | 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 assignments were made using AutoAssign software. Sidechain assignments were completed manually. Initial NOESY assignments for the monomer were made using AutoStructure and CYANA-2.1. The oligomeric state was confirmed to be a monomer by measuring the correlation time using 1D T1 and T2 experiments. A total of 100 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Final structure quality factors were determined using the PSVS server: ordered residues are defined as (7-18 and 24-61). (a) RMSD (ordered residues) all backbone atoms: 0.6A; all heavy atoms: 0.9A. (b) Ramachandran statistics for all ordered residues: Most favoured region: 87.2%; additionally allowed region: 12.4%; generously allowed region: 0.3% and disallowed region: 0.0%. (c) Procheck scores for all ordered residues (Raw/Z) phi/psi -0.81/-2.87; all dihedral angles: -0.45/-2.66. (d) MolProbity clash score (Raw/Z): 13.47/-0.79. (e) RPF scores for the goodness of fit to NOESY data:- Recall: 0.888; precision: 0.968; F-measure: 0.926; DP score: 0.821 | AutoAssign |
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 | chemical shift assignment | AutoAssign | 2.2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
2 | chemical shift assignment | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
3 | structure solution | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
4 | geometry optimization | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
5 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
6 | geometry optimization | CNS | 2.0.6 | Brunger, Adams, Clore, Gros, Nilges and Read |
7 | refinement | CNS | 2.0.6 | Brunger, Adams, Clore, Gros, Nilges and Read |
8 | peak picking | Sparky | 2.1 | Goddard |