2BNZ Dna Binding Protein Dna date Apr 06, 2005
title Structural Basis For Cooperative Binding Of Ribbon-Helix- Helix Omega Repressor To Inverted Dna Heptad Repeats
authors W.A.Weihofen, A.Cicek, F.Pratto, J.C.Alonso, W.Saenger
compound source
Molecule: Orf Omega
Chain: A, B, C, D
Fragment: Ribbon-Helix-Helix Domain, Residues 20-71
Synonym: Omega Transcriptional Repressor, Orf Omega'
Engineered: Yes
Organism_scientific: Streptococcus Pyogenes
Organism_taxid: 1314
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a-Delta19omega
Other_details: Omega Transcriptional Repressor Is Encoded B Plasmid Psm19035 Of The Inc18 Family Of Plasmids;

Molecule: 5'-D(Gpapaptpcpapcpapapgp Tpgpaptptpapgpc)-3';
Chain: E, G
Other_details: Sequence\: 5'- Gaa Tca Caa Gtg Att Agc -3', Dna Oligonucleotide, First Strand, Inverted Dna Heptad Rep (5'- Aatcac At -3'), Nucleotides G5 - G16, G18 And E18 We Modelled;

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Inverted Repeats Occur In Promoter Regions P Genes Controlled By Omega Transcriptional Repressor, Plasm Psm19035;

Molecule: 5'-D(Cptpapaptpcpapcptptp Gptpgpaptptpcpg)-3';
Chain: F, H
Other_details: Sequence\: 5'- Cta Atc Act Tgt Gat Tcg -3', Dna Oligonucleotide, Second Strand, Nucleotides H19 - H31 Modelled

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Inverted Repeats Occur In Promoter Regions P Genes Controlled By Omega Transcriptional Repressor, Plasm Psm19035
symmetry Space Group: P 1 21 1
R_factor 0.225 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.991 42.505 103.727 90.00 107.17 90.00
method X-Ray Diffractionresolution 2.60 Å
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription., Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W, Nucleic Acids Res. 2006 Mar 9;34(5):1450-8. Print 2006. PMID:16528102
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (2bnz.pdb1.gz) 51 Kb
  • CSU: Contacts of Structural Units for 2BNZ
  • Likely Quarternary Molecular Structure file(s) for 2BNZ
  • Structure Factors (140 Kb)
  • Retrieve 2BNZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BNZ from S2C, [Save to disk]
  • Re-refined 2bnz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BNZ 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 2BNZ
  • 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 2BNZ, from MSDmotif at EBI
  • Fold representative 2bnz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bnz_G] [2bnz_B] [2bnz_D] [2bnz_E] [2bnz_H] [2bnz_C] [2bnz_A] [2bnz] [2bnz_F]
  • SWISS-PROT database: [Q57468]
  • Domain organization of [Q57468_STRPY] by SWISSPFAM
  • Other resources with information on 2BNZ
  • Community annotation for 2BNZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science