1O9R Iron-Binding Protein date Dec 18, 2002
title The X-Ray Crystal Structure Of Agrobacterium Tumefaciens Dps Of The Family That Protect Dna Without Binding
authors A.Ilari, P.Ceci, E.Chiancone
compound source
Molecule: Agrobacterium Tumefaciens Dps
Chain: A, B, C, D, E, F
Synonym: Dna-Binding Protein, Dps-At
Engineered: Yes
Organism_scientific: Agrobacterium Tumefaciens
Organism_taxid: 358
Strain: Gv3101
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet11-A
symmetry Space Group: P 21 21 2
R_factor 0.170 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.046 90.349 105.656 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand EDO, FE, TRS enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceThe Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: x-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties., Ceci P, Ilari A, Falvo E, Chiancone E, J Biol Chem 2003 May 30;278(22):20319-26. PMID:12660233
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (166 Kb) [Save to disk]
  • Biological Unit Coordinates (1o9r.pdb1.gz) 320 Kb
  • LPC: Ligand-Protein Contacts for 1O9R
  • CSU: Contacts of Structural Units for 1O9R
  • Likely Quarternary Molecular Structure file(s) for 1O9R
  • Structure Factors (1286 Kb)
  • Retrieve 1O9R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1O9R from S2C, [Save to disk]
  • Re-refined 1o9r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1O9R 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 1O9R
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1O9R 1O9RA 1O9RB 1O9RC 1O9RD 1O9RE 1O9RF from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1O9R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o9ra_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1o9rb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1o9rc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1o9rd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1o9re_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1o9rf_, region F [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1o9r] [1o9r_F] [1o9r_D] [1o9r_C] [1o9r_B] [1o9r_A] [1o9r_E]
  • SWISS-PROT database: [Q8UCK6]
  • Domain organization of [DPS_AGRT5] by SWISSPFAM
  • Other resources with information on 1O9R
  • Community annotation for 1O9R at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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