2AXD
solution structure of the theta subunit of escherichia coli DNA polymerase III in complex with the epsilon subunit
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_15N-separated_NOESY | 1MM THETA-EPSILON186 U15N,13C(THETA); 100mM NaCl, 0.1mM DITHIOTHREITOL; 20mM PHOSPHATE BUFFER Na; 90% H20, 10% D2O | 90% H20, 10% D2O | 100mM NaCl | 7.0 | ambient | 298 | |
2 | 3D_15N-separated_NOESY | 1MM THETA-EPSILON186 U15N,13C(THETA); 100mM NaCl, 0.1mM DITHIOTHREITOL; 20mM TRIS BUFFER; 90% H20, 10% D2O | 90% H20, 10% D2O | 100mM NaCl | 7.0 | ambient | 298 | |
3 | 3D_13C-separated_NOESY | 1MM THETA-EPSILON186 U15N,13C(THETA); 100mM NaCl, 0.1mM DITHIOTHREITOL; 20mM PHOSPHATE BUFFER Na; 90% H20, 10% D2O | 90% H20, 10% D2O | 100mM NaCl | 7.0 | ambient | 298 | |
4 | 3D_13C-separated_NOESY | 1MM THETA-EPSILON186 U15N,13C(THETA); 100mM NaCl, 0.1mM DITHIOTHREITOL; 20mM TRIS BUFFER; 90% H20, 10% D2O | 90% H20, 10% D2O | 100mM NaCl | 7.0 | ambient | 298 | |
5 | HNHA | 1MM THETA-EPSILON186 U15N,13C(THETA); 100mM NaCl, 0.1mM DITHIOTHREITOL; 20mM PHOSPHATE BUFFER Na; 90% H20, 10% D2O | 90% H20, 10% D2O | 100mM NaCl | 7.0 | ambient | 298 | |
6 | 2D_15N-HSQC | 1MM THETA-EPSILON186 U15N,13C(THETA); 100mM NaCl, 0.1mM DITHIOTHREITOL; 20mM TRIS BUFFER; 90% H20, 10% D2O | 90% H20, 10% D2O | 100mM NaCl | 7.0 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | INOVA | 800 |
3 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle dynamics | THE STRUCTURES ARE BASED ON 632 DISTANCE RESTRAINTS, 111 DIHEDRAL ANGLE RESTRAINTS AND 162 PSEUDO-CONTACT SHIFT RESTRAINTS. THE PSEUDO-CONTACT SHIFTS WERE CALCULATED FROM THE CHANGE IN CHEMICAL SHIFT OF THE AMIDE PROTONS INDUCED BY INSERTING A LANTHANIDE ION (EITHER YSPROSIUM, ERBIUM OR HOLMIUM) AT THE METAL BINDING SITE OF EPSILON-186 WHICH IS COMPLEXED TO THE THETA SUBUNIT. XPLOR-NIH 2.9.7 WAS USED TO REFINE THE STRUCTURE USING THIS DATA | VNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 12 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | THE STRUCTURE WAS DETERMINED USING DISTANCE AND ANGULAR RESTRAINTS AND SUPPLEMENTED WITH RESTRAINTS CALCULATED FROM PSEUDO-CONTACT SHIFTS INDUCED BY INSERTING A LANTHANIDE ION INTO THE EPSILON186 BINDING POCKET |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | VNMR | 6.1 | VARIAN ASSOCIATES |
2 | data analysis | XEASY | 1.4 | C.BARTELS, T.XIA, M.BILLETER, P.GUENTERT, K.WUETHRICH |
3 | data analysis | Sparky | 3.110 | T.GODDARD, D.KNELLER |
4 | refinement | DYANA | 1.5 | P.GUENTERT |
5 | refinement | XPLOR-NIH | 2.9.7 | C.SCHWIETERS, N.TJANDRA, J.KUSZEWSKI, G.CLORE |