3ORY Hydrolase date Sep 08, 2010
title Crystal Structure Of Flap Endonuclease 1 From Hyperthermophi Archaeon Desulfurococcus Amylolyticus
authors T.Mase, K.Kubota, K.Miyazono, Y.Kawarabayashii, M.Tanokura
compound source
Molecule: Flap Endonuclease 1
Chain: A
Engineered: Yes
 Organism_scientific: Desulfurococcus Amylolyticus
Organism_taxid: 94694
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 3 2 1
R_factor 0.210 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.760 103.760 84.580 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity
  • exonuclease activity
  • 5'-3' exonuclease activity


    • Primary referenceStructure of flap endonuclease 1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus., Mase T, Kubota K, Miyazono K, Kawarabayasi Y, Tanokura M, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Feb 1;67(Pt, 2):209-13. Epub 2011 Jan 21. PMID:21301087
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (3ory.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (3ory.pdb2.gz) 336 Kb
  • LPC: Ligand-Protein Contacts for 3ORY
  • CSU: Contacts of Structural Units for 3ORY
  • Structure Factors (515 Kb)
  • Retrieve 3ORY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ORY from S2C, [Save to disk]
  • Re-refined 3ory structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3ORY 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 3ORY
  • 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 3ORY, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ory_A] [3ory]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3ORY: [HhH2] [XPGI] [XPGN ] by SMART
    • Other resources with information on 3ORY
  • Community annotation for 3ORY 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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