1SQR
Solution Structure of the 50S Ribosomal Protein L35AE from Pyrococcus furiosus. Northeast Structural Genomics Consortium Target PfR48.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D 13C-NOESY (aliphatic), HCCH-COSY | 1.07 MM PfR48 U-15N,13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.5 | 95% H2O/5% D2O | 100 mM | 6.5 | ambient | 293 | |
2 | 3D 13C-NOESY (aliphatic and aromatic), 13C,1H-HSQC | 1.07 MM PfR48 U-15N,13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.5 | 100% D2O | 100 mM | 6.5 | ambient | 293 | |
3 | 4D_13C-separated_NOESY | 1.07 MM PfR48 U-15N,13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.5 | 100% D2O | 100 mM | 6.5 | ambient | 293 | |
4 | 3D-TOCSYs | 1.07 MM PfR48 U-15N,13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.5 | 95% H2O/5% D2O | 100 mM | 6.5 | ambient | 293 | |
5 | H/D EXCHANGE | 0.5 MM PfR48 U-15N 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.5 | 95% H2O/5% D2O | 100 mM | 6.5 | ambient | 293 | |
6 | 3D 15N-NOESY, backbone TR experiments | 0.1 MM PfR48 U-15N,5%-13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.5 | 95% H2O/5% D2O | 100 mM | 6.5 | ambient | 293 | |
7 | high-resolution/non-constant-time 13C,1H-HSQC | 1.07 MM PfR48 U-15N,13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.5 | 95% H2O/5% D2O | 100 mM | 6.5 | ambient | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 800 |
2 | Varian | INOVA | 750 |
3 | Varian | INOVA | 600 |
4 | Varian | UNITY | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | THE STRUCTURES ARE BASED ON A TOTAL OF 1157 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE RESTRAINTS, 177 DIHEDRAL ANGLE RESTRAINTS, AND 32 HYDROGEN BOND RESTRAINTS. (14.4 CONSTRAINTS PER RESIDUE; 6.1 LONG-RANGE RESTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR). THE UNSTRUCTURED 8 RESIDUE C-TERMINAL TAG (LEHHHHHH) WAS INCLUDED IN THE STRUCTURE CALCULATIONS BUT IS OMITTED FROM THIS DEPOSITION. | X-PLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 56 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS. BACKBONE DIHEDRAL ANGLES FOR RESIDUES 1, 13-20, 26-27, 39-40, 47-51, 54, 63-66 AND 73-79 ARE NOT WELL-DEFINED [S(PHI) + S(PSI) < 1.8] IN THIS SOLUTION NMR STRUCTURE. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | NIH 2.0.6 | Schwieters, et al. |
2 | collection | VNMR | 6.1B | Varian |
3 | processing | NMRPipe | 2.1 | Delaglio, et al. |
4 | data analysis | Sparky | 3.106 | Goddard |
5 | structure solution | PdbStat | 3.32 | Tejero and Montelione |
6 | refinement | AutoStructure | 2.0.0 | Huang and Montelione |
7 | structure solution | HYPER | 3.2 | Tejero and Montelione |
8 | data analysis | AutoAssign | 1.9 | Zimmerman, Moseley and Montelione |
9 | structure solution | TALOS | 2.1 | Cornilescu, Delaglio and Bax |