4F6N Dna Binding Protein Dna date May 15, 2012
title Crystal Structure Of Kaiso Zinc Finger Dna Binding Protein I With Methylated Cpg Site Dna
authors B.A.Buck-Koehntop, R.L.Stanfield, D.C.Ekiert, M.A.Martinez-Yamo H.J.Dyson, I.A.Wilson, P.E.Wright
compound source
Molecule: Transcriptional Regulator Kaiso
Chain: A
Fragment: Zinc Finger Dna Binding Domain
Synonym: Zinc Finger And Btb Domain-Containing Protein 33
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Zbtb33, Kaiso, Znf348
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)[Dnay]
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21d

Molecule: Dna (5'-D(Gptpgptpcpapcp(5cm)Pgp(5cm) Pgptpcptpaptpapcpg)-3');
Chain: D
Engineered: Yes
Other_details: Meecad Dna Strand 1

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Other_details: This Sequence Occurs In Humans

Molecule: Dna (5'-D(Cpgptpaptpapgpap(5cm)Pgp(5cm Pgpgptpgpapcpapc)-3');
Chain: E
Engineered: Yes
Other_details: Meecad Dna Strand 2

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Other_details: This Sequence Occurs In Humans
symmetry Space Group: F 2 2 2
R_factor 0.228 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.049 183.402 230.138 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 5CM, GOL, ZN enzyme
Primary referenceMolecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso., Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE, Proc Natl Acad Sci U S A. 2012 Sep 4. PMID:22949637
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (4f6n.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 4F6N
  • CSU: Contacts of Structural Units for 4F6N
  • Structure Factors (180 Kb)
  • Retrieve 4F6N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4F6N from S2C, [Save to disk]
  • Re-refined 4f6n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4F6N 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 4F6N
  • 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 4F6N, from MSDmotif at EBI
  • Fold representative 4f6n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4f6n_A] [4f6n_E] [4f6n_D] [4f6n]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4F6N: [ZnF_C2H2 ] by SMART
  • Other resources with information on 4F6N
  • Community annotation for 4F6N at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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