3VYB	Hydrolase Dna	date	Sep 22, 2012
title	Crystal Structure Of Methyl Cpg Binding Domain Of Mbd4 In Co The 5mcghmcg Sequence
authors	J.Otani, K.Arita, T.Kato, M.Kinoshita, M.Ariyoshi, M.Shirakawa
compound		source
Molecule: Methyl-Cpg-Binding Domain Protein 4 Chain: A Fragment: Methyl Cpg Binding Domain, Unp Residues 69-136 Synonym: Methyl-Cpg-Binding Protein Mbd4, Mismatch-Specific Glycosylase; Ec: 3.2.2.- Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Gene: Mbd4 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid
Molecule: Dna (5'-D(Gptpcpapcptpapcp(5cm)Pgpgpa 3'); Chain: B Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Gptpcp(5hc)Pgpgptpapgptpgpa 3'); Chain: C Engineered: Yes		Synthetic: Yes
symmetry	Space Group: C 2 2 21	R_factor 0.191 R_Free 0.220
crystal cell	length a length b length c angle alpha angle beta angle gamma 88.693 97.758 55.725 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	5CM, 5HC, ACT, EDO	enzyme	Hydrolase E.C.3.2.2 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4., Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M, J Biol Chem. 2013 Mar 1;288(9):6351-62. doi: 10.1074/jbc.M112.431098. Epub 2013, Jan 10. PMID:23316048

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk] Biological Unit Coordinates (3vyb.pdb1.gz) 46 Kb LPC: Ligand-Protein Contacts for 3VYB CSU: Contacts of Structural Units for 3VYB Structure Factors (151 Kb) Retrieve 3VYB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3VYB from S2C, [Save to disk] Re-refined 3vyb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

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Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3VYB, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3vyb_A] [3vyb_B] [3vyb] [3vyb_C] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3VYB: [MBD ] by SMART

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