5FDK Hydrolase date Dec 16, 2015
title Crystal Structure Of Recu(D88n) In Complex With Palindromic
authors S.Khavnekar, J.B.Rafferty, A.Kale
compound source
Molecule: Holliday Junction Resolvase Recu
Chain: A, B, C, D
Ec: 3.1.22.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Recu, Prfa, Yppb, Bsu22310
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcb210

Molecule: Palindromic Dna
Chain: E, F, G, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: H 3 2
R_factor 0.256 R_Free 0.329
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.447 144.447 310.343 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.21 Å
ligand
enzyme Hydrolase E.C.3.1.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • nuclease activity
  • endonuclease activity


  • Primary referenceStructural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state., Khavnekar S, Dantu SC, Sedelnikova S, Ayora S, Rafferty J, Kale A, Nucleic Acids Res. 2016 Nov 29. pii: gkw1165. PMID:27903910
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (5fdk.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (5fdk.pdb2.gz) 74 Kb
  • CSU: Contacts of Structural Units for 5FDK
  • Structure Factors (1435 Kb)
  • Retrieve 5FDK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FDK from S2C, [Save to disk]
  • Re-refined 5fdk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5FDK 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 5FDK
  • 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 5fdk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5fdk_E] [5fdk_G] [5fdk_A] [5fdk_H] [5fdk_D] [5fdk_C] [5fdk_B] [5fdk_F] [5fdk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5FDK
  • Community annotation for 5FDK at PDBWiki (http://pdbwiki.org)

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