2BNW Dna-Binding Regulatory Protein date Apr 05, 2005
title Structural Basis For Cooperative Binding Of Ribbon-Helix-Hel Repressor To Direct 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_common: Streptococcus
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 Psm19035 Of The Inc18 Family Of Plasmids;

Molecule: 5'-D(Gpapaptpcpapcpapapap Tpcpapcpapapgpc)-3';
Chain: E, G
Engineered: Yes
Other_details: Sequence\: 5'- Gaa Tca Caa Atc Aca Agc -3', Oligonucleotide, First Strand, Direct Dna Heptad Repeats (5 -3');

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Direct Dna Heptad Repeats Occur In Promoters Preceeding Genes Controlled By Omega Transcriptional Epress Family Of Plasmids;

Molecule: 5'-D(Cptptpgptpgpaptptptp Gptpgpaptptpcpg)-3';
Chain: F, H
Engineered: Yes
Other_details: Sequence\: 5'- Ctt Gtg Att Tgt Gat Tcg -3', Oligonucleotide, Second Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Direct Dna Heptad Repeats Occur In Promoters Preceeding Genes Controlled By Omega Transcriptional Epress Family Of Plasmids
symmetry Space Group: C 1 2 1
R_factor 0.226 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
219.426 44.631 75.960 90.00 108.80 90.00
method X-Ray Diffractionresolution 2.45 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] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (2bnw.pdb1.gz) 62 Kb
  • CSU: Contacts of Structural Units for 2BNW
  • Likely Quarternary Molecular Structure file(s) for 2BNW
  • Structure Factors (194 Kb)
  • Retrieve 2BNW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BNW from S2C, [Save to disk]
  • Re-refined 2bnw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BNW 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 2BNW
  • 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 2BNW, from MSDmotif at EBI
  • Fold representative 2bnw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bnw_F] [2bnw_D] [2bnw_B] [2bnw_C] [2bnw_E] [2bnw] [2bnw_H] [2bnw_A] [2bnw_G]
  • SWISS-PROT database: [Q57468]
  • Domain organization of [Q57468_STRPY] by SWISSPFAM
  • Other resources with information on 2BNW
  • Community annotation for 2BNW 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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