3OR3 Hydrolase Dna date Sep 06, 2010
title Restriction Endonuclease Hpy188i In Complex With Product Dna
authors M.Sokolowska, H.Czapinska, M.Bochtler
compound source
Molecule: Restriction Endonuclease Hpy188i
Chain: A, B
Engineered: Yes
 Organism_scientific: Helicobacter Pylori
Organism_common: Campylobacter Pylori
Organism_taxid: 585532
Strain: 188
Gene: Hpy188ir, Synthetic Gene Codon Optimized For Escheric
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Er2566
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15bmod

Molecule: 5'-D(Gpaptpcpt)-3'
Chain: C
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: 5'-D(Gptptpcpa)-3'
Chain: D
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: 5'-D(Pgpapapc)-3'
Chain: E
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: 5'-D(Pgpaptpc)-3'
Chain: F
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide
symmetry Space Group: P 41 21 2
R_factor 0.168 R_Free 0.201
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.395 65.395 221.783 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CA, CL, MSE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • endonuclease activity


    • Primary referenceHpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis., Sokolowska M, Czapinska H, Bochtler M, Nucleic Acids Res. 2010 Oct 8. PMID:20935048
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (172 Kb) [Save to disk]
  • Biological Unit Coordinates (3or3.pdb1.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 3OR3
  • CSU: Contacts of Structural Units for 3OR3
  • Structure Factors (252 Kb)
  • Retrieve 3OR3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OR3 from S2C, [Save to disk]
  • Re-refined 3or3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3OR3 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 3OR3
  • 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
  • 3D motif for 3OR3, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3or3] [3or3_C] [3or3_F] [3or3_E] [3or3_D] [3or3_B] [3or3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3OR3
  • Community annotation for 3OR3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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