2LP6
Refined Solution NMR Structure of the 50S ribosomal protein L35Ae from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target (NESG) PfR48
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 | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
2 | 2D 1H-13C HSQC aliphatic | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
3 | 2D 1H-13C HSQC aromatic | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
4 | 3D HNCO | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
5 | 3D CBCA(CO)NH | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
6 | 3D HNCACB | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
7 | 3D HBHA(CO)NH | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
8 | 3D CCC(CO)NH TOCSY | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
9 | 3D HCCH-TOCSY | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
10 | 3D HCCH-COSY | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
11 | 3D HNHA | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
12 | 3D 1H-15N NOESY | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
13 | 3D 1H-13C NOESY aliphatic | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 100% D2O | 6.5 | ambient | 293 | ||
14 | 3D 1H-13C NOESY aromatic | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
15 | 3D 1H-13C NOESY aliphatic | 1.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | ambient | 293 | ||
16 | 2D 1H-13C HSQC high resolution | 0.29 mM [U-5% 13C; U-100% 15N] PfR48.002, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS | 90% H2O/10% D2O | 6.5 | 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 |
simulated annealing | THE FINAL REFINED STRUCTURES ARE BASED ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (18.3 CONSTRAINTS PER RESIDUE, 7.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 91 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS 1.3) WITH PARAM19. | CNS |
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) |
Additional NMR Experimental Information | |
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Details | THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN, FOLLOWED BY MANUAL SIDE CHAIN ASSIGNMENT. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus, AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING THE C-TERMINAL HIS6): BACKBONE, 98.2%, SIDE CHAIN, 90.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 84.2%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 91, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,21-76,79-87: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.0. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 97.0%, ADDITIONALLY ALLOWED, 3.0%, DISALLOWED, 0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.56/-1.89, ALL, -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.13/-1.07 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 91): RECALL, 0.965, PRECISION, 0.878, F-MEASURE, 0.920, DP-SCORE, 0.784. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 5. THE FINAL FOUR UNASSIGNED HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1,13-20,77-78,88-91. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | CNS | 1.3 | Brunger, Adams, Clore, Gros, Nilges and Read |
2 | structure solution | CNS | 1.3 | Brunger, Adams, Clore, Gros, Nilges and Read |
3 | geometry optimization | CNS | 1.3 | Brunger, Adams, Clore, Gros, Nilges and Read |
4 | structure solution | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
5 | data analysis | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
6 | data analysis | AutoAssign | 1.9 | Zimmerman, Moseley, Kulikowski and Montelione |
7 | chemical shift assignment | AutoAssign | 1.9 | Zimmerman, Moseley, Kulikowski and Montelione |
8 | processing | NMRPipe | 2.3 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
9 | collection | VNMR | 6.1B | Varian |
10 | data analysis | Sparky | 3 | Goddard |
11 | structure solution | TALOS+ | Shen, Cornilescu, Delaglio and Bax | |
12 | data analysis | PSVS | 1.4 | Bhattacharya, Montelione |
13 | data analysis | PdbStat | 5.5 | Tejero, Montelione |
14 | data analysis | MolProbity | 3.19 | Richardson |