7KW8 | pdb_00007kw8

NMR Structure of a tRNA 2'-phosphotransferase from Runella slithyformis


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D 1H-15N NOESY300 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % v/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
23D 1H-13C NOESY aliphatic360 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % v/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
33D 1H-13C NOESY aromatic300 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 1 mM AEBSF protease inhibitor, 0.05 % w/v sodium azide, 50 uM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 700
43D 1H-13C NOESY aromatic400 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.05 % w/v sodium azide, 50 mM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
53D 1H-13C Methyl NOESY400 uM [U-2H; U-15N];[13CD1,1H3]ILE;[13CD1,1H3;13CD2,1H3]LEU;[13CG1,1H3;13CG2,1H3]VAL;[13CE1,1H3]MET;[13CG2,1H3]THR Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.05 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III 600
61H-13C-13C-1H 4D NOESY350 uM [U-2H; U-15N];[13CD1,1H3]ILE;[13CD1,1H3;13CD2,1H3]LEU;[13CG1,1H3;13CG2,1H3]VAL;[13CE1,1H3]MET;[13CG2,1H3]THR Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.05 % w/v sodium azide, 50 uM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
73D HNCA420 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
83D HNCO380 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
93D HN(CA)CO380 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
103D CBCA(CO)NH380 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
113D HNCACB380 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
123D C(CO)NH380 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
133D H(CCO)NH380 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS95% H2O/5% D2O071 atm290.15Bruker AVANCE III HD 800
143D CCH-TOCSY400 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
153D HCCH-TOCSY400 uM [U-13C; U-15N] Tpt1, 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 2 mM [U-100% 2H] EDTA, 5 % v/v [U-100% 2H] glycerol, 0.5 mM AEBSF protease inhibitor, 0.04 % w/v sodium azide, 50 mM DSS100% D2O071 atm290.15Bruker AVANCE III HD 800
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III HD800
2BrukerAVANCE III HD700
3BrukerAVANCE III600
4BrukerAVANCE III HD800
NMR Refinement
MethodDetailsSoftware
simulated annealingthe structures are based on a total of 2997 restraints, 2587 are NOE-derived distance constraints, 278 dihedral angle restraints, 132 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