3QMB Dna Binding Protein Dna date Feb 04, 2011
title Structural Basis Of Selective Binding Of Nonmethylated Cpg I The Cxxc Domain Of Cfp1
authors R.Lam, C.Xu, C.B.Bian, J.Kania, C.Bountra, J.Weigelt, C.H.Arrowsmi A.M.Edwards, A.Bochkarev, J.Min, Structural Genomics Consortiu
compound source
Molecule: Cpg-Binding Protein
Chain: A
Fragment: Cxxc-Type Zn Finger, Residues 161-222
Synonym: Cxxc-Type Zinc Finger Protein 1, Phd Finger And Cx Containing Protein 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cfp1, Cgbp, Cxxc1, Pccx1, Phf18
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21-(De3)-V2r-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl

Molecule: 5'-D(Gpcpcpapcpcpgpgptpgpgpc)-3'
Chain: B, C
Fragment: Dna (Nonmethylated Cpg Island)
Engineered: Yes

Synthetic: Yes
Other_details: Dna Was Purchased From Integrated Dna Techno Inc.
symmetry Space Group: C 2 2 21
R_factor 0.220 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
37.375 71.965 115.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.06 Å
ligand CA, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain., Xu C, Bian C, Lam R, Dong A, Min J, Nat Commun. 2011 Mar;2:227. PMID:21407193
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (3qmb.pdb1.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 3QMB
  • CSU: Contacts of Structural Units for 3QMB
  • Structure Factors (230 Kb)
  • Retrieve 3QMB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QMB from S2C, [Save to disk]
  • Re-refined 3qmb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QMB 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 3QMB
  • 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
  • 3D motif for 3QMB, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qmb_B] [3qmb] [3qmb_A] [3qmb_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3QMB
  • Community annotation for 3QMB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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