5AEW Oxidoreductase date Jan 10, 2015
title Crystal Structure Of Ii9 Variant Of Biphenyl Dioxygenase From Burkholderia Xenovorans Lb400 In Complex With Biphenyl
authors S.Dhindwal, L.Gomez-Gil, M.Sylvestre, L.D.Eltis, J.T.Bolin, P.Kum
compound source
Molecule: Biphenyl Dioxygenase Subunit Beta
Chain: B, D, F, H, J, L, N, P, R, T, V, X
Synonym: Biphenyl 2,3-Dioxygenase, Biphenyl Dioxygease
Ec: 1.14.12.18
Engineered: Yes
Mutation: Yes
Organism_scientific: Burkholderia Xenovorans Lb400
Organism_taxid: 266265
Variant: Ii9
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: C41
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet14b

Molecule: Biphenyl Dioxygenase Subunit Alpha
Chain: A, C, E, G, I, K, M, O, Q, S, U, W
Synonym: Biphenyl 2,3-Dioxygenase, Biphenyl Dioxygease
Ec: 1.14.12.18
Engineered: Yes
Mutation: Yes

Organism_scientific: Burkholderia Xenovorans Lb400
Organism_taxid: 266265
Variant: Ii9
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: C41
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet14b
symmetry Space Group: P 1
R_factor 0.22485 R_Free 0.26300
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.767 133.191 133.965 102.31 102.54 104.54
method X-Ray Diffractionresolution 1.88 Å
ligand BNL, FE2, FES enzyme Oxidoreductase E.C.1.14.12.18 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, T, N, V, L, J, X, P, B, H, D, R


S, K, E, Q, M, C, A, O, W, I, G, U


Primary referenceStructural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase., Dhindwal S, Gomez-Gil L, Neau DB, Pham TT, Sylvestre M, Eltis LD, Bolin JT, Kumar P, J Bacteriol. 2016 Apr 28;198(10):1499-512. doi: 10.1128/JB.00952-15. Print 2016, May 15. PMID:26953337
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2521 Kb) [Save to disk]
  • Biological Unit Coordinates (5aew.pdb1.gz) 657 Kb
  • Biological Unit Coordinates (5aew.pdb2.gz) 636 Kb
  • Biological Unit Coordinates (5aew.pdb3.gz) 635 Kb
  • Biological Unit Coordinates (5aew.pdb4.gz) 631 Kb
  • Biological Unit Coordinates (5aew.pdb5.gz) 629 Kb
  • LPC: Ligand-Protein Contacts for 5AEW
  • CSU: Contacts of Structural Units for 5AEW
  • Structure Factors (12249 Kb)
  • Retrieve 5AEW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5AEW from S2C, [Save to disk]
  • Re-refined 5aew structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5AEW 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 5AEW
  • 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
  • Fold representative 5aew from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5aew_J] [5aew_R] [5aew_L] [5aew_C] [5aew_P] [5aew_G] [5aew_H] [5aew_I] [5aew_A] [5aew_U] [5aew_F] [5aew_O] [5aew_N] [5aew_Q] [5aew_V] [5aew_X] [5aew] [5aew_D] [5aew_S] [5aew_B] [5aew_E] [5aew_K] [5aew_M] [5aew_W] [5aew_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5AEW
  • Community annotation for 5AEW at PDBWiki (http://pdbwiki.org)

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