4K9P Lyase date Apr 20, 2013
title Crystal Structure Of The His281tyrala460ile Double Mutant O Benzoylformate Decarboxylase From Pseudomonas Putida
authors H.R.Brodkin, M.J.Mcleish
compound source
Molecule: Benzoylformate Decarboxylase
Chain: A, B, C, D
Synonym: Bfd, Bfdc
Engineered: Yes
Mutation: Yes
Organism_scientific: Pseudomonas Putida
Organism_taxid: 303
Gene: Mdlc
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24
symmetry Space Group: P 21 21 21
R_factor 0.173 R_Free 0.201
length a length b length c angle alpha angle beta angle gamma
70.769 164.546 175.881 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.24 Å
ligand CA, GOL, MG, TPP enzyme Lyase E.C. BRENDA
A, D, C, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (348 Kb) [Save to disk]
  • Biological Unit Coordinates (4k9p.pdb1.gz) 340 Kb
  • LPC: Ligand-Protein Contacts for 4K9P
  • CSU: Contacts of Structural Units for 4K9P
  • Structure Factors (954 Kb)
  • Retrieve 4K9P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4K9P from S2C, [Save to disk]
  • Re-refined 4k9p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4K9P 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 4K9P
  • 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
  • 3D motif for 4K9P, from MSDmotif at EBI
  • Fold representative 4k9p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4k9p_D] [4k9p_A] [4k9p_C] [4k9p] [4k9p_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4K9P
  • Community annotation for 4K9P at PDBWiki (http://pdbwiki.org)

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