3W6V	Transcription Activator Dna	date	Feb 22, 2013
title	Crystal Structure Of The Dna-Binding Domain Of Adpa, The Glo Transcriptional Factor, In Complex With A Target Dna
authors	M.D.Yao, J.Ohtsuka, K.Nagata, K.Miyazono, Y.Ohnishi, M.Tanokura
compound		source
Molecule: Adpa Chain: A Fragment: Dna-Binding Domain, Residues 215-340 Engineered: Yes		Organism_scientific: Streptomyces Griseus Organism_taxid: 1911 Gene: Adpa Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-28a
Molecule: Dna (5'-D(Cptpgptpgpapapcpcpcpgpcpcp 3'); Chain: B Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Apgpgptptpgpgpcpgpgpgptptp 3'); Chain: C Engineered: Yes		Synthetic: Yes
symmetry	Space Group: C 2 2 21	R_factor 0.236 R_Free 0.278
crystal cell	length a length b length c angle alpha angle beta angle gamma 76.510 100.640 100.910 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.95 Å
Gene Ontology	Chain Function Process Component A
Primary reference	Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity., Yao MD, Ohtsuka J, Nagata K, Miyazono K, Zhi Y, Ohnishi Y, Tanokura M, J Biol Chem. 2013 Oct 25;288(43):31019-29. doi: 10.1074/jbc.M113.473611. Epub, 2013 Sep 9. PMID:24019524

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk] Biological Unit Coordinates (3w6v.pdb1.gz) 31 Kb CSU: Contacts of Structural Units for 3W6V Structure Factors (116 Kb) Retrieve 3W6V in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3W6V from S2C, [Save to disk] Re-refined 3w6v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3W6V 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 3W6V

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 3D motif for 3W6V, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3w6v_A] [3w6v_B] [3w6v] [3w6v_C] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3W6V: [HTH_ARAC ] by SMART

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Community annotation for 3W6V at PDBWiki (http://pdbwiki.org)

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