2LXF
Solution NMR structure of a potential acylphosphatase from Giardia lamblia, Seattle Structural Genomics Center for Infectious Disease target GilaA.01396.a
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 | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
2 | 3D HNCACB | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
3 | 3D CBCA(CO)NH | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
4 | 3D HNCO | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
5 | 3D 1H-15N NOESY | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
6 | 3D 1H-13C NOESY aliphatic | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
7 | 3D 1H-13C NOESY aromatic | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
8 | 3D C(CO)NH | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
9 | 2D 1H-13C HSQC aliphatic | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
10 | 2D 1H-13C HSQC aromatic | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 93% H2O/7% D2O | 0.12 | 7 | ambient | 293 | |
11 | 2D 1H-15N HSQC | 1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT | 100% D2O | 0.12 | 7 | ambient | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | INOVA | 750 |
3 | Varian | INOVA | 800 |
NMR Refinement | ||
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Method | Details | Software |
DGSA-distance geometry simulated annealing | STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 5% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS. | Sparky |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | Sparky | 3.115 | Goddard |
2 | peak picking | Sparky | 3.115 | Goddard |
3 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
4 | processing | Felix | 2007 | Accelrys Software Inc. |
5 | refinement | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
6 | data analysis | PSVS | 1.3 | Bhattacharya and Montelione |