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 Diffractionresolution 2.95 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceComplex 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) 32 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
  • 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 3W6V, from MSDmotif at EBI
  • Fold representative 3w6v from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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
  • Other resources with information on 3W6V
  • Community annotation for 3W6V at PDBWiki (http://pdbwiki.org)

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