5D4S	Transcription Dna	date	Aug 08, 2015
title	Crystal Structure Of Arar(Dbd) In Complex With Operator Orx1
authors	D.Jain, N.Narayanan, D.T.Nair
compound		source
Molecule: Arabinose Metabolism Transcriptional Repressor Chain: A, B Fragment: Unp Residues 1-68 Engineered: Yes		Organism_scientific: Bacillus Subtilis (Strain 168) Organism_taxid: 224308 Strain: 168 Gene: Arar, Arac, Yvbs, Bsu33970 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pdjn1
Molecule: Dna (5'- D(Tpapaptpaptptptpgptpapcpgptpaptpgptpap 3'); Chain: T Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Dna (5'- D(Apapaptpapcpaptpapcpgptpapcpapapaptpap 3'); Chain: U Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: C 1 2 1	R_factor 0.195 R_Free 0.241
crystal cell	length a length b length c angle alpha angle beta angle gamma 138.228 42.454 67.211 90.00 114.99 90.00
method	X-Ray Diffraction	resolution	1.97 Å
Gene Ontology	Chain Function Process Component A, B
Primary reference	Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators., Jain D, Narayanan N, Nair DT, J Biol Chem. 2016 Jan 15;291(3):1235-42. doi: 10.1074/jbc.M115.689695. Epub 2015 , Oct 28. PMID:26511320

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk] Biological Unit Coordinates (5d4s.pdb1.gz) 87 Kb CSU: Contacts of Structural Units for 5D4S Structure Factors (364 Kb) Retrieve 5D4S in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5D4S from S2C, [Save to disk] Re-refined 5d4s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D4S 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 5D4S

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Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5d4s] [5d4s_A] [5d4s_U] [5d4s_B] [5d4s_T] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5D4S: [HTH_GNTR ] by SMART

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