2KY8

Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
23D HNCO1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
33D HNCA1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
43D HN(CO)CA1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
53D HNCACB1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
63D CBCA(CO)NH1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
73D HCCH-TOCSY1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
83D C(CO)NH1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
93D C(CO)NH1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
103D CCH-TOCSY1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
113D 1H-15N NOESY1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
123D 1H-15N NOESY1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
133D 1H-13C NOESY1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
142D 13C,15N filtered NOESY1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
152D 1H-15N HSQC0.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage90% H2O/10% D2O206.5ambient298
162D 1H-15N HSQC-T10.5 mM [U-13C; U-15N; U-2H] cMBD2, 0.5 mM DNA, 0.5 mM MANGANESE (II) ION90% H2O/10% D2O206.5ambient298
172D 1H-15N HSQC-T10.5 mM [U-13C; U-15N; U-2H] cMBD2, 0.5 mM DNA, 0.5 mM CA2+90% H2O/10% D2O206.5ambient298
183D-HNCO-JNH0.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage90% H2O/10% D2O206.5ambient298
193D-HNCO-JNH1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
202D 1H-15N HSQC,JNCO1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
212D 1H-15N HSQC.JNCO0.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage90% H2O/10% D2O206.5ambient298
223D HNCO,JCOCA1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA90% H2O/10% D2O206.5ambient298
233D HNCO,JCOCA0.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage90% H2O/10% D2O206.5ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianUNITYPLUS500
2BrukerAVANCE700
NMR Refinement
MethodDetailsSoftware
torsion angle dynamicsexperimental target function included NOE distances, backbone torsion angle restraints based on chemical shifts, residual dipolar couplings and paramagnetic relaxation enhancement data.X-PLOR NIH
NMR Ensemble Information
Conformer Selection Criteriaall calculated structures submitted
Conformers Calculated Total Number20
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementX-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore
2chemical shift assignmentPIPPGarrett
3peak pickingPIPPGarrett
4processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5collectionTopSpinBruker Biospin
6collectionVNMRVarian