2KVS
NMR Solution Structure of Q7A1E8 protein from Staphylococcus aureus: Northeast Structural Genomics Consortium target: ZR215
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 | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
2 | 2D 1H-13C HSQC | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
3 | 3D CBCA(CO)NH | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
4 | 3D HNCACB | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
5 | 3D HBHA(CO)NH | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
6 | 3D HNCO | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
7 | 3D HNHA | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
8 | 3D HCCH-TOCSY | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
9 | 3D 1H-15N NOESY | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
10 | 3D 1H-13C NOESY | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 293 | |
11 | 2D 1H-15N HNOE | 0.71 mM [U-100% 13C; U-100% 15N] ZR215-1 | 90% H2O/10% D2O | 100mM NaCl | 7.5 | ambient | 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 | 400 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Initial dihedral angle constriants were obtained from TALOS. Final quality factors determined using PSVS software. Ordered residues were defined as 8-12,18-30,35-37,43-77.RMSD(ordered residues):Backbone 1.0A, All atoms 1.5A; Ramachandran statistics for all ordered regions: Most favored regions: 91.5%; Additionally allowed: 8.4% and generously allowed: 0.1%. Procheck scores for all ordered residues are (Raw/Z): phi-psi 0.11/0.75 All:0.04/0.24; MolProbity clash score(Raw/Z):13.45/-0.78; RPF scores for goodness of fit of NOESY data: Recall: 0.954; Precision:0.928; F-measure: 0.941; DP-score 0.798. | AutoAssign |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 400 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | The structure was determined using triple resonance NMR spectroscopy. Automated resonance assignments were made using AutoAssign. Sidechain assignments were completed manually. Chemical shift assignments were validated using AVS software. Automated NOESY assignments were made using AutoStructure and structure solution was determined using CYANA-2.1. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | AutoAssign | 2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
2 | processing | NMRPipe | 2008 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
3 | peak picking | Sparky | 2.3 | Goddard |
4 | data analysis | Sparky | 2.3 | Goddard |
5 | collection | VnmrJ | 2.1B | Varian |
6 | collection | TopSpin | 2.1 | Bruker Biospin |
7 | structure solution | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
8 | data analysis | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
9 | geometry optimization | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
10 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
11 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
12 | chemical shift validation | AVS | Moseley and Montelione | |
13 | structure validation | PSVS | 1.3 | Bhattacharya and Montelione |
14 | dihedral angle constriants | TALOS | Cornilescu, Delaglio and Bax |