3URP Hydrolase date Nov 22, 2011
title Re-Refinement Of Pdb Entry 5rnt - Ribonuclease T1 With Guano 5'-Diphosphate And Phosphate Ion Bound
authors O.S.Smart, T.O.Womack, C.Flensburg, P.Keller, A.Sharff, W.Paciore C.Vonrhein, G.Bricogne
compound source
Molecule: Guanyl-Specific Ribonuclease T1
Chain: A
Synonym: Rnase T1
Ec: 3.1.27.3
 Organism_scientific: Aspergillus Oryzae
Organism_taxid: 5062
symmetry Space Group: I 2 3
R_factor 0.202 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.470 86.470 86.470 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.19 Å
ligand PGP, PO4, UNX enzyme Hydrolase E.C.3.1.27.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity
  • ribonuclease activity


    • Primary referenceExploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER., Smart OS, Womack TO, Flensburg C, Keller P, Paciorek W, Sharff A, Vonrhein C, Bricogne G, Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):368-80. Epub 2012 Mar 16. PMID:22505257
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (22 Kb) [Save to disk]
  • Biological Unit Coordinates (3urp.pdb1.gz) 18 Kb
  • LPC: Ligand-Protein Contacts for 3URP
  • CSU: Contacts of Structural Units for 3URP
  • Structure Factors (69 Kb)
  • Retrieve 3URP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3URP from S2C, [Save to disk]
  • Re-refined 3urp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3URP 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 3URP
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3URP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3urp_A] [3urp]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3URP
  • Community annotation for 3URP at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science