5HNF Hydrolase date Jan 18, 2016
title Crystal Structure Of Pyrene- And Phenanthrene-Modified Dna I With The Bpuj1 Endonuclease Binding Domain
authors M.Probst, W.Aeschimann, T.T.H.Chau, S.M.Langenegger, A.Stocker
compound source
Molecule: Restriction Endonuclease R.Bpuji
Chain: A
Engineered: Yes
Organism_scientific: Bacillus Pumilus
Organism_taxid: 1408
Gene: Bpujir
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Gp(Ype)Papcpcpcpgptpgpgpa)-3
Chain: L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Tpcpcpapcpgpgpgptp(Ypf)Pc)-3
Chain: M
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.171 R_Free 0.196
crystal
cell
length a length b length c angle alpha angle beta angle gamma
165.723 59.278 44.048 90.00 94.20 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand YPE, YPF enzyme
Primary referenceStructural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease., Probst M, Aeschimann W, Chau TT, Langenegger SM, Stocker A, Haner R, Nucleic Acids Res. 2016 Sep 6;44(15):7079-89. doi: 10.1093/nar/gkw644. Epub 2016 , Jul 15. PMID:27422870
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk]
  • Biological Unit Coordinates (5hnf.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 5HNF
  • CSU: Contacts of Structural Units for 5HNF
  • Structure Factors (1620 Kb)
  • Retrieve 5HNF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HNF from S2C, [Save to disk]
  • Re-refined 5hnf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5HNF 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 5HNF
  • 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 5hnf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5hnf_A] [5hnf_L] [5hnf] [5hnf_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5HNF
  • Community annotation for 5HNF at PDBWiki (http://pdbwiki.org)

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