4EVV Hydrolase Dna date Apr 26, 2012
title Mouse Mbd4 Glycosylase Domain In Complex With A G:T Mismatch
authors H.Hashimoto, X.Zhang, X.Cheng
compound source
Molecule: Methyl-Cpg-Binding Domain Protein 4
Chain: A
Fragment: Glycosylase Domain, Unp Residues 411-554
Synonym: Methyl-Cpg-Binding Protein Mbd4, Mismatch-Specific Glycosylase;
Ec: 3.2.2.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Mbd4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pxc1064

Molecule: Dna (5'-D(Tpcpapgpcpgpcpaptpgpg)-3')
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Dna Synthesis

Molecule: Dna (5'-D(Cpcpaptpgptpgpcptpgpa)-3')
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Dna Synthesis
symmetry Space Group: C 2 2 21
R_factor 0.258 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.690 110.770 119.240 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.39 Å
ligand EDO, NI enzyme Hydrolase E.C.3.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceExcision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation., Hashimoto H, Zhang X, Cheng X, Nucleic Acids Res. 2012 Jun 27. PMID:22740654
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (4evv.pdb1.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 4EVV
  • CSU: Contacts of Structural Units for 4EVV
  • Structure Factors (166 Kb)
  • Retrieve 4EVV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4EVV from S2C, [Save to disk]
  • Re-refined 4evv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4EVV in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4EVV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4EVV, from MSDmotif at EBI
  • Fold representative 4evv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4evv] [4evv_C] [4evv_A] [4evv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4EVV
  • Community annotation for 4EVV at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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