7KW9 | pdb_00007kw9

NMR Structure of a tRNA 2'-phosphotransferase from Runella slithyformis in complex with NAD+


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D HNCO600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 600
23D HN(CA)CO600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 600
33D HNCA280 uM [U-13C; U-15N] Tpt1, 1.12 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
43D HN(CO)CA600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 700
53D HNCACB600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 700
63D CBCA(CO)NH280 uM [U-13C; U-15N] Tpt1, 1.12 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
73D HBHA(CO)NH600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III 700
83D C(CO)NH600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 600
93D H(CCO)NH600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 600
103D CCH-TOCSY325 uM [U-13C; U-15N] Tpt1, 1.3 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
113D HCCH-TOCSY325 uM [U-13C; U-15N] Tpt1, 1.3 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
122D 1H-1H NOESY300 uM [U-13C; U-15N] Tpt1, 1.2 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
133D 1H-15N NOESY500 uM [U-13C; U-15N; U-2H] Tpt1, 2 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE II 900
143D 1H-15N NOESY600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
153D 1H-13C NOESY aromatic600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
163D 1H-13C NOESY aromatic325 uM [U-13C; U-15N] Tpt1, 1.3 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
173D 1H-13C NOESY aliphatic600 uM [U-13C; U-15N] Tpt1, 2.4 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 700
183D 1H-13C NOESY aliphatic325 uM [U-13C; U-15N] Tpt1, 1.3 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
193D 1H-13C NOESY methyl300 uM [U-13C; U-15N] Tpt1, 1.2 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III HD 700
204D 1H-13C-13C-1H NOESY methyl400 uM [U-13C; U-15N] Tpt1, 1.6 mM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-2H] EDTA, 5 % v/v [U-2H] glycerol, 1 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III HD600
2BrukerAVANCE III HD700
3BrukerAVANCE III HD800
5BrukerAVANCE III700
4BrukerAVANCE III HD800
6BrukerAVANCE II900
NMR Refinement
MethodDetailsSoftware
simulated annealingthe structures are based on a total of 3773 restraints, 3368 are NOE-derived distance constraints, 269 dihedral angle restraints, 136 from hydrogen bonds.X-PLOR NIH
NMR Ensemble Information
Conformer Selection Criteriastructures with acceptable covalent geometry
Conformers Calculated Total Number100
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingNMRPipe10.3 Revision 2019.220.13.40Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2collectionTopSpin3.5p15Bruker Biospin
3chemical shift assignmentNMRViewJohnson, One Moon Scientific
4structure calculationARIA2.3.2Linge, O'Donoghue and Nilges
5refinementX-PLOR NIH2.52Schwieters, Kuszewski, Tjandra and Clore