4IHT Transcription Dna date Dec 19, 2012
title Crystal Structure Of Benm_dbdbena Site 1 Dna Complex
authors A.Alanazi, C.Momany, E.L.Neidle
compound source
Molecule: Hth-Type Transcriptional Regulator Benm
Chain: A, B, C, D
Fragment: Unp Residues 1-87
Synonym: Ben And Cat Operon Transcriptional Regulator, Transcriptional Regulator Benm Dna Binding Domain;
Engineered: Yes
Organism_scientific: Acinetobacter Sp.
Organism_taxid: 62977
Strain: Adp1
Gene: Aciad1435, Benm, Benr
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b

Molecule: Bena Site 1 Dna
Chain: E, G
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna Purchased From Idt

Molecule: Bena Site 1 Dna - Complement
Chain: F, H
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna Purchased From Idt
symmetry Space Group: P 21 21 2
R_factor 0.185 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
58.956 300.295 46.003 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
A, D, C, B

Primary referenceThe DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators., Alanazi AM, Neidle EL, Momany C, Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):1995-2007. doi:, 10.1107/S0907444913017320. Epub 2013 Sep 20. PMID:24100318
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (394 Kb) [Save to disk]
  • Biological Unit Coordinates (4iht.pdb1.gz) 193 Kb
  • Biological Unit Coordinates (4iht.pdb2.gz) 194 Kb
  • CSU: Contacts of Structural Units for 4IHT
  • Structure Factors (394 Kb)
  • Retrieve 4IHT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IHT from S2C, [Save to disk]
  • Re-refined 4iht structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IHT 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 4IHT
  • 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 4IHT, from MSDmotif at EBI
  • Fold representative 4iht from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4iht_A] [4iht_C] [4iht] [4iht_H] [4iht_F] [4iht_G] [4iht_B] [4iht_D] [4iht_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4IHT
  • Community annotation for 4IHT at PDBWiki (http://pdbwiki.org)

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