3EGM Oxidoreductase date Sep 11, 2008
title Structural Basis Of Iron Transport Gating In Helicobacter Py Ferritin
authors K.H.Kim, K.J.Cho, H.J.Shin, J.H.Lee
compound source
Molecule: Ferritin
Chain: A, B, C, D, E, F
Ec: 1.16.3.1
Engineered: Yes
Organism_scientific: Helicobacter Pylori
Organism_common: Campylobacter Pylori J99
Organism_taxid: 85963
Strain: J99
Gene: Ftna, Pfr, Jhp_0598
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet
symmetry Space Group: I 4
R_factor 0.162 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
128.528 128.528 165.380 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand FE, GOL enzyme Oxidoreductase E.C.1.16.3.1 BRENDA
Gene JHP
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceThe crystal structure of ferritin from Helicobacter pylori reveals unusual conformational changes for iron uptake., Cho KJ, Shin HJ, Lee JH, Kim KJ, Park SS, Lee Y, Lee C, Park SS, Kim KH, J Mol Biol. 2009 Jul 3;390(1):83-98. Epub 2009 May 7. PMID:19427319
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (363 Kb) [Save to disk]
  • Biological Unit Coordinates (3egm.pdb1.gz) 1421 Kb
  • LPC: Ligand-Protein Contacts for 3EGM
  • CSU: Contacts of Structural Units for 3EGM
  • Likely Quarternary Molecular Structure file(s) for 3EGM
  • Structure Factors (1247 Kb)
  • Retrieve 3EGM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EGM from S2C, [Save to disk]
  • Re-refined 3egm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EGM 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 3EGM
  • 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 3EGM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3egm_B] [3egm_A] [3egm_D] [3egm_E] [3egm_F] [3egm_C] [3egm]
  • SWISS-PROT database: [Q9ZLI1]
  • Domain organization of [FTN_HELPJ] by SWISSPFAM
  • Other resources with information on 3EGM
  • Community annotation for 3EGM 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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