3WHN Metal Binding Protein date Aug 29, 2013
title Hemerythrin-Like Domain Of Dcrh I119h Mutant (Met)
authors Y.Okamoto, A.Onoda, H.Sugimoto, Y.Takano, S.Hirota, D.M.Kurtz Jr. T.Hayashi
compound source
Molecule: Hemerythrin-Like Domain Protein Dcrh
Chain: A, B
Engineered: Yes
Mutation: Yes
 Organism_scientific: Desulfovibrio Vulgaris
Organism_taxid: 882
Strain: Hildenborough
Gene: Dcrh
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-16b
symmetry Space Group: P 1
R_factor 0.193 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
33.573 44.082 46.715 92.71 102.59 90.02
method X-Ray Diffractionresolution 1.90 Å
ligand CA, CFO enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceHO-dependent substrate oxidation by an engineered diiron site in a bacterial hemerythrin., Okamoto Y, Onoda A, Sugimoto H, Takano Y, Hirota S, Kurtz DM, Shiro Y, Hayashi T, Chem Commun (Camb). 2014 Jan 8. PMID:24400317
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (3whn.pdb1.gz) 27 Kb
  • Biological Unit Coordinates (3whn.pdb2.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 3WHN
  • CSU: Contacts of Structural Units for 3WHN
  • Structure Factors (386 Kb)
  • Retrieve 3WHN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WHN from S2C, [Save to disk]
  • Re-refined 3whn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3WHN 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 3WHN
  • 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 3WHN, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3whn_A] [3whn] [3whn_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3WHN
  • Community annotation for 3WHN at PDBWiki (http://pdbwiki.org)

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