5HLK Hydrolase Dna date Jan 15, 2016
title Crystal Structure Of The Ternary Ecorv-Dna-Lu Complex With C Substrate.
authors S.S.Sangani, A.D.Kehr, K.Sinha, G.S.Rule, L.Jen-Jacobson
compound source
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

Molecule: Dna (5'-D(Apapapgpaptp)-3')
Chain: C, D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Aptpcptptptp)-3')
Chain: E, F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.166 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.621 48.327 63.531 96.94 108.78 106.70
method X-Ray Diffractionresolution 2.00 Å
ligand EDO, LU, NA enzyme Hydrolase E.C.3.1.21.4 BRENDA
note 5HLK supersedes 4ORJ
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 (5hlk.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 5HLK
  • CSU: Contacts of Structural Units for 5HLK
  • Structure Factors (640 Kb)
  • Retrieve 5HLK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HLK from S2C, [Save to disk]
  • Re-refined 5hlk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5HLK 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 5HLK
  • 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: [5hlk_A] [5hlk] [5hlk_D] [5hlk_E] [5hlk_C] [5hlk_F] [5hlk_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5HLK
  • Community annotation for 5HLK at PDBWiki (http://pdbwiki.org)

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