2HJJ
Solution NMR structure of protein ykfF from Escherichia coli. Northeast Structural Genomics target ER397.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_13C-separated_NOESY | 0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5 | 5% D2O / 95% H2O | 100 mM NaCl | 5.5 | ambient | 293 | |
2 | 3D_15N-separated_NOESY | 0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5 | 5% D2O / 95% H2O | 100 mM NaCl | 5.5 | ambient | 293 | |
3 | 3D_13C-separated_NOESY | 0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5 | 100% D2O | 100 mM NaCl | 5.5 | ambient | 293 | |
4 | HNHA | 0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5 | 5% D2O / 95% H2O | 100 mM NaCl | 5.5 | ambient | 293 | |
5 | high resolution CH-HSQC (stereospecific assignment of Val/Leu methyls) | 0.95 mM 5%-13C,U-15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5 | 5% D2O / 95% H2O | 100 mM NaCl | 5.5 | ambient | 293 | |
6 | 3D GFT backbone expts | 0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5 | 5% D2O / 95% H2O | 100 mM NaCl | 5.5 | ambient | 293 | |
7 | 3D HCCH-COSY and HCCH-TOCSYs | 0.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5 | 5% D2O / 95% H2O | 100 mM NaCl | 5.5 | 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 | THE STRUCTURES ARE BASED ON A TOTAL OF 1044 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 72 DIHEDRAL ANGLE CONSTRAINTS, AND 52 HYDROGEN BOND CONSTRAINTS (17.7 CONSTRAINTS PER RESIDUE, 5.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 10 to 75 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE UNSTRUCTURED N- AND C- TERMINI OF THE PROTEIN WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. | VNMR |
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 STRUCTURE WAS DETERMINED USING GFT AND TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE FROM THE GFT DATA USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 95.3%, SIDE CHAIN, 93.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 90.9%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 10 TO 75, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 11-67,72-74: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 85.9%, ADDITIONALLY ALLOWED, 13.8%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.1%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.45/-1.46, ALL, -0.38/-2.25. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 29.98/-3.62. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.956, PRECISION, 0.934, F-MEASURE, 0.945, DP-SCORE, 0.848. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | VNMR | 6.1C | Varian |
2 | collection | TopSpin | 1.3 | Bruker |
3 | refinement | AutoAssign | 2.1.1 | Zimmerman, Moseley, Montelione |
4 | refinement | XPLOR-NIH | 2.11.2 | Clore et al |
5 | refinement | AutoStructure | 2.1.1 | Huang & Montelione |
6 | processing | AGNuS | 2.0 | Moseley & Montelione |
7 | data analysis | PdbStat | 4.1 | Tejero & Montelione |
8 | data analysis | PSVS | 1.3 | Bhattacharya, Hang, Montelione |
9 | refinement | CNS | 1.1 | Brunger et al |