5F8A Hydrolase Dna date Dec 09, 2015
title Crystal Structure Of The Ternary Ecorv-Dna-Lu Complex With U Dna Substrate. Lanthanide Binding To Ecorv-Dna Complex Inhi Cleavage.
authors S.S.Sangani, A.D.Kehr, K.Sinha, G.S.Rule, L.Jen-Jacobson
compound source
Molecule: Dna (5'-D(Apapapgpaptpaptpcptptpt)-3'
Chain: C, D
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Type-2 Restriction Enzyme Ecorv
Chain: A, B
Synonym: R.Ecorv,Endonuclease Ecorv,Type II Restriction Enz
Ec: 3.1.21.4
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Ecorvr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.160 R_Free 0.199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.430 52.860 65.310 70.61 73.24 81.81
method X-Ray Diffractionresolution 1.76 Å
ligand EDO, LU, NA enzyme Hydrolase E.C.3.1.21.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


    • Primary referenceMetal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex., Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson L, Biochemistry. 2016 Oct 27. PMID:27786446
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (5f8a.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 5F8A
  • CSU: Contacts of Structural Units for 5F8A
  • Structure Factors (1160 Kb)
  • Retrieve 5F8A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F8A from S2C, [Save to disk]
  • Re-refined 5f8a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5F8A 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 5F8A
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f8a_D] [5f8a_B] [5f8a_A] [5f8a] [5f8a_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5F8A
  • Community annotation for 5F8A at PDBWiki (http://pdbwiki.org)

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