3DR9 Oxidoreductase date Jul 10, 2008
title Increased Distal Histidine Conformational Flexibility In The Form Of Dehaloperoxidase From Amphitrite Ornata
authors X.Chen, V.S.De Serrano, L.Betts, S.Franzen
compound source
Molecule: Dehaloperoxidase A
Chain: A, B
Engineered: Yes
 Organism_scientific: Amphitrite Ornata
Organism_taxid: 129555
Gene: Dhpa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16b
symmetry Space Group: P 21 21 21
R_factor 0.174 R_Free 0.196
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.517 67.194 69.094 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.26 Å
ligand HEM, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • peroxidase activity


    • Primary referenceDistal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata., Chen Z, de Serrano V, Betts L, Franzen S, Acta Crystallogr D Biol Crystallogr. 2009 Jan;65(Pt 1):34-40. Epub 2008, Dec 18. PMID:19153464
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (3dr9.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (3dr9.pdb2.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 3DR9
  • CSU: Contacts of Structural Units for 3DR9
  • Likely Quarternary Molecular Structure file(s) for 3DR9
  • Structure Factors (576 Kb)
  • Retrieve 3DR9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DR9 from S2C, [Save to disk]
  • Re-refined 3dr9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DR9 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 3DR9
  • 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 3DR9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dr9] [3dr9_A] [3dr9_B]
  • SWISS-PROT database: [Q9NAV8]
  • Domain organization of [Q9NAV8_9ANNE] by SWISSPFAM
    • Other resources with information on 3DR9
  • Community annotation for 3DR9 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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