7D3V | pdb_00007d3v

Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3A


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D HNCO25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Bruker AVANCE 900
23D HNCACB25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Bruker AVANCE 900
33D HNCA25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Bruker AVANCE 900
43D HN(CO)CA25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Bruker AVANCE 900
53D CBCA(CO)NH25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Bruker AVANCE 900
63D 1H-15N NOESY25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Bruker AVANCE 900
73D 1H-15N TOCSY25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Bruker AVANCE 900
82D 1H-15N HSQC25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Bruker AVANCE 900
92D 1H-13C HSQC25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA100% D2O375 mM7.31 atm293Bruker AVANCE 900
103D HCCH-TOCSY25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA100% D2O375 mM7.31 atm293Bruker AVANCE 900
113D 1H-13C NOESY aliphatic25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA100% D2O375 mM7.31 atm293Bruker AVANCE 900
123D 1H-13C NOESY aromatic25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA100% D2O375 mM7.31 atm293Bruker AVANCE 900
132D filter TOCSY25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA100% D2O375 mM7.31 atm293Agilent DD2 800
142D filter NOESY25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA100% D2O375 mM7.31 atm293Agilent DD2 800
153D 15N-filter-edit NOESY25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA90% H2O/10% D2O375 mM7.31 atm293Agilent DD2 800
163D 13C-filter-edit NOESY25 mM sodium phosphate, 200 mM sodium chloride, 50 uM Zinc chloride, 5 mM DTT, 0.28 mM [U-13C; U-15N] A3A, 0.56 mM DNA100% D2O375 mM7.31 atm293Agilent DD2 800
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE900
2AgilentDD2800
NMR Refinement
MethodDetailsSoftware
simulated annealingCNS
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number100
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2chemical shift assignmentSparkyGoddard
3structure calculationX-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore
4refinementCNSBrunger, Adams, Clore, Gros, Nilges and Read