5XXP Dna Binding Protein date Jul 04, 2017
title Crystal Structure Of Cbnr_dbd-Dna Complex
authors T.Senda, M.Senda
compound source
Molecule: Lysr-Type Regulatory Protein
Chain: A, B
Fragment: Unp Residues 1-87
Engineered: Yes
Organism_scientific: Cupriavidus Necator
Organism_common: Alcaligenes Eutrophus
Organism_taxid: 106590
Gene: Cbnr, Bjn34_37375
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (25-Mer)
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Cupriavidus Necator
Organism_taxid: 106590

Molecule: Dna (25-Mer)
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Cupriavidus Necator
Organism_taxid: 106590
symmetry Space Group: C 1 2 1
R_factor 0.219 R_Free 0.263
length a length b length c angle alpha angle beta angle gamma
186.457 28.719 73.153 90.00 111.65 90.00
method X-Ray Diffractionresolution 2.55 Å
A, B

Primary referenceCrystal structure of the DNA-binding domain of the LysR-type transcriptional regulator CbnR in complex with a DNA fragment of the recognition-binding site in the promoter region., Koentjoro MP, Adachi N, Senda M, Ogawa N, Senda T, FEBS J. 2018 Jan 11. doi: 10.1111/febs.14380. PMID:29323785
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (5xxp.pdb1.gz) 47 Kb
  • CSU: Contacts of Structural Units for 5XXP
  • Structure Factors (164 Kb)
  • Retrieve 5XXP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XXP from S2C, [Save to disk]
  • View 5XXP 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 5XXP
  • 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
  • Fold representative 5xxp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xxp_B] [5xxp_A] [5xxp_F] [5xxp_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XXP
  • Community annotation for 5XXP at PDBWiki (http://pdbwiki.org)

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