2JQQ
Solution structure of Saccharomyces cerevisiae conserved oligomeric Golgi subunit 2 protein (Cog2p)
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D HNCO | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 | |
2 | 3D HNCACB | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 | |
3 | 3D CBCA(CO)NH | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 | |
4 | 2D DQF-COSY | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 100% D2O | 0.01 | 7 | ambient | 303 | |
5 | 2D 1H-15N HSQC | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 | |
6 | 3D HCCH-TOCSY | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 | |
7 | 3D C(CO)NH | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 | |
8 | 3D 1H-15N NOESY | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 | |
9 | 3D 1H-13C NOESY | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 | |
10 | 2D 1H-13C CT-HSQC | 1 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide | 95% H2O/5% D2O | 0.01 | 7 | ambient | 303 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 800 |
2 | Varian | INOVA | 750 |
3 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
DGSA-distance geometry simulated annealing | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 1200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | Experiments collected at the EMSL at PNNL. Residues 59-108 were present in the Cog2 protein used in this NMR study; however a lack of long-range contacts prevented the inclusion of these residues in the final models. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | CNS | 1.1 | A Brunger, P Adams, M Clore, P Gros, M Nilges and R Read |
2 | refinement | CNS | 1.1 | A Brunger, P Adams, M Clore, P Gros, M Nilges and R Read |
3 | processing | NMRPipe | F Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Bax | |
4 | refinement | AQUA | T Rullmann, JF Doreleijers and R Kaptein | |
5 | peak picking | NMRView | B Johnson, One Moon Scientific | |
6 | chemical shift assignment | NMRView | B Johnson, One Moon Scientific | |
7 | data analysis | NMRView | B Johnson, One Moon Scientific | |
8 | geometry optimization | TALOS | G Cornilescu, F Delaglio and A Bax | |
9 | collection | XwinNMR | Bruker Biospin | |
10 | refinement | ProcheckNMR | RA Laskowski and M MacArthur |