BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 16936

Title: Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence   PubMed: 21531701

Authors: Williams, David; Scarsdale, Joe

Citation: Scarsdale, J. Neel; Webb, Heather; Ginder, Gordon; Williams, David. "Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence."  Nucleic Acids Res. 39, 6741-6752 (2011).

Assembly members:
cMBD2, polymer, 72 residues, 7861.131 Da.
DNA-strand_1, polymer, 11 residues, 2794.885 Da.
DNA-strand_2, polymer, 11 residues, 3044.045 Da.
MN, non-polymer, 54.938 Da.

Natural source:   Common Name: chicken   Taxonomy ID: 9031   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Gallus gallus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
cMBD2: GSDKQGRTDCPALPPGWKKE EVIRKSGLSAGKSDVYYFSP SGKKFRSKPQLARYLGNAVD LSCFDFRTGKMM
DNA-strand_1: GGAATXGGCXC
DNA-strand_2: GAGCXGATXCC

Data sets:
Data typeCount
13C chemical shifts307
15N chemical shifts70
1H chemical shifts582

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1cMBD21
2DNA-strand_12
3DNA-strand_23
4MANGANESE (II) ION_14
5MANGANESE (II) ION_24

Entities:

Entity 1, cMBD2 72 residues - 7861.131 Da.

1   GLYSERASPLYSGLNGLYARGTHRASPCYS
2   PROALALEUPROPROGLYTRPLYSLYSGLU
3   GLUVALILEARGLYSSERGLYLEUSERALA
4   GLYLYSSERASPVALTYRTYRPHESERPRO
5   SERGLYLYSLYSPHEARGSERLYSPROGLN
6   LEUALAARGTYRLEUGLYASNALAVALASP
7   LEUSERCYSPHEASPPHEARGTHRGLYLYS
8   METMET

Entity 2, DNA-strand_1 11 residues - 2794.885 Da.

1   DGDGDADADT5CMDGDGDCTHY
2   DC

Entity 3, DNA-strand_2 11 residues - 3044.045 Da.

1   DGDADGDC5CMDGDADTTHYDC
2   DC

Entity 4, MANGANESE (II) ION_1 - Mn - 54.938 Da.

1   MN

Samples:

sample_1: cMBD2, [U-99% 13C; U-99% 15N], 1 mM; DNA-strand_1 1 mM; DNA-strand_2 1 mM; phosphate 10 mM; sodium azide 0.02%; D20 10%; H20 90%

phage_alignment: cMBD2, [U-13C; U-15N; U-2H], 0.8 mM; DNA-strand_1 0.8 mM; DNA-strand_2 0.8 mM; pf1 bacteriophage 12 mg/mL; phosphate 10 mM; sodium azide 0.02%; D20 10%; H20 90%

PRE_sample_MN: cMBD2, [U-13C; U-15N; U-2H], 0.5 mM; DNA-strand_1 0.5 mM; DNA-strand_2 0.5 mM; MANGANESE (II) ION 0.5 mM; phosphate 10 mM; sodium azide 0.02%; D20 10%; H20 90%

PRE_sample_CA: cMBD2, [U-13C; U-15N; U-2H], 0.5 mM; DNA-strand_1 0.5 mM; DNA-strand_2 0.5 mM; CA2+ 0.5 mM; phosphate 10 mM; sodium azide 0.02%; D20 10%; H20 90%

sample_conditions_1: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D 13C,15N filtered NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCphage_alignmentanisotropicsample_conditions_1
2D 1H-15N HSQC-T1PRE_sample_MNisotropicsample_conditions_1
2D 1H-15N HSQC-T1PRE_sample_CAisotropicsample_conditions_1
3D-HNCO-JNHphage_alignmentanisotropicsample_conditions_1
3D-HNCO-JNHsample_1isotropicsample_conditions_1
2D 1H-15N HSQC,JNCOsample_1isotropicsample_conditions_1
2D 1H-15N HSQC.JNCOphage_alignmentanisotropicsample_conditions_1
3D HNCO,JCOCAsample_1isotropicsample_conditions_1
3D HNCO,JCOCAphage_alignmentanisotropicsample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

PIPP, Garrett - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN, Bruker Biospin - collection

VNMR, Varian - collection

NMR spectrometers:

  • Varian UnityPlus 500 MHz
  • Bruker Avance 700 MHz

Related Database Links:

GB NP_001012403 AAC68872 AAC68874 AAD50372 AAD50373 AAH46607
PDB
REF NP_001012403 NP_001108497 NP_001298000 NP_034903 XP_005074763
SP Q9Z2E1