BMRB Entry 19391

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19391
MolProbity Validation Chart

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Title:
Solution structure of MBD3 methylcytosine binding domain while bound to hydroxymethylated DNA
Deposition date:
2013-07-26
Original release date:
2013-12-09
Authors:
Williams, David; Scarsdale, J.
Citation:

Citation: Cramer, Jason; Scarsdale, J. Neel; Walavalkar, Ninad; Buchwald, William; Ginder, Gordon; Williams, David. "Probing the Dynamic Distribution of Bound States for Methylcytosine-binding Domains on DNA."  J. Biol. Chem. 289, 1294-1302 (2014).
PubMed: 24307175

Assembly members:

Assembly members:
MBD3, polymer, 72 residues, 8342.584 Da.
hDNA_A, polymer, 17 residues, Formula weight is not available
hDNA_B, polymer, 17 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET32a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MBD3: GSMERKRWECPALPQGWERE EVPRRSGLSAGHRDVFYYSP SGKKFRSKPQLARYLGGSMD LSTFDFRTGKML
hDNA_A: GAGGCGCTXGGCGGCAG
hDNA_B: CTGCCGCXGAGCGCCTC

Data sets:
Data typeCount
13C chemical shifts309
15N chemical shifts68
1H chemical shifts437

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1MBD3 methylcytosine binding domain1
2Hydroxymethylated DNA A Strand2
3Hydroxymethylated DNA B Strand3

Entities:

Entity 1, MBD3 methylcytosine binding domain 72 residues - 8342.584 Da.

1   GLYSERMETGLUARGLYSARGTRPGLUCYS
2   PROALALEUPROGLNGLYTRPGLUARGGLU
3   GLUVALPROARGARGSERGLYLEUSERALA
4   GLYHISARGASPVALPHETYRTYRSERPRO
5   SERGLYLYSLYSPHEARGSERLYSPROGLN
6   LEUALAARGTYRLEUGLYGLYSERMETASP
7   LEUSERTHRPHEASPPHEARGTHRGLYLYS
8   METLEU

Entity 2, Hydroxymethylated DNA A Strand 17 residues - Formula weight is not available

1   DGDADGDGDCDGDCDT5HCDG
2   DGDCDGDGDCDADG

Entity 3, Hydroxymethylated DNA B Strand 17 residues - Formula weight is not available

1   DCDTDGDCDCDGDC5HCDGDA
2   DGDCDGDCDCDTDC

Samples:

sample_1: MBD3, [U-99% 13C; U-99% 15N], 0.5 – 1.0 mM; hDNA_A0.6 – 1.1 mM; hDNA_B0.6 – 1.1 mM; H2O 90%; D2O 10%

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 CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

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

CCPN, Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, and Laue - data analysis

NMR spectrometers:

  • Bruker Avance 700 MHz

Related Database Links:

PDB
DBJ BAF83571 BAI46781
GB AAC68876 AAC68877 AAC72104 AAD48909 EAW69477
REF NP_001102205 NP_001180972 NP_001268382 NP_038623 XP_002723919
SP O95983 Q9Z2D8
AlphaFold O95983 Q9Z2D8

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks