4MTD Dna Binding Protein Dna date Sep 19, 2013
title Zinc Uptake Regulator Complexed With Zinc And Dna
authors B.A.Gilston, A.Mondragon, T.V.O'Halloran
compound source
Molecule: Zinc Uptake Regulation Protein
Chain: A, B, C, D
Synonym: Zinc Uptake Regulator
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: B4046, Jw5714, Yjbk, Zur
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24d

Molecule: Znuabc Operator Dna
Chain: Y
Engineered: Yes

Synthetic: Yes

Molecule: Znuabc Operator Dna
Chain: Z
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.234 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
193.324 80.470 98.770 90.00 120.15 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural and Mechanistic Basis of Zinc Regulation Across the E. coli Zur Regulon., Gilston BA, Wang S, Marcus MD, Canalizo-Hernandez MA, Swindell EP, Xue Y, Mondragon A, O'Halloran TV, PLoS Biol. 2014 Nov 4;12(11):e1001987. doi: 10.1371/journal.pbio.1001987., eCollection 2014 Nov. PMID:25369000
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk]
  • Biological Unit Coordinates (4mtd.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 4MTD
  • CSU: Contacts of Structural Units for 4MTD
  • Structure Factors (1572 Kb)
  • Retrieve 4MTD in mmCIF format [Save to disk]
  • Re-refined 4mtd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4MTD 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 4MTD
  • 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 4MTD, from MSDmotif at EBI
  • Fold representative 4mtd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4mtd_A] [4mtd_C] [4mtd] [4mtd_B] [4mtd_Z] [4mtd_Y] [4mtd_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4MTD
  • Community annotation for 4MTD at PDBWiki (http://pdbwiki.org)

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