4QBO Hydrolase date May 08, 2014
title Vrr_nuc Domain
authors S.J.Smerdon, S.Pennell, J.Li
compound source
Molecule: Nuclease
Chain: A
Engineered: Yes
 Organism_scientific: Streptococcus Phage P9
Organism_taxid: 403905
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.172 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.854 60.517 81.137 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity


    • Primary referenceFAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain., Pennell S, Declais AC, Li J, Haire LF, Berg W, Saldanha JW, Taylor IA, Rouse J, Lilley DM, Smerdon SJ, Cell Rep. 2014 Jul 10;8(1):84-93. doi: 10.1016/j.celrep.2014.06.001. Epub 2014, Jun 26. PMID:24981866
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (4qbo.pdb1.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 4QBO
  • CSU: Contacts of Structural Units for 4QBO
  • Structure Factors (261 Kb)
  • Retrieve 4QBO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4QBO from S2C, [Save to disk]
  • Re-refined 4qbo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4QBO 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 4QBO
  • 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
  • 3D motif for 4QBO, from MSDmotif at EBI
  • Fold representative 4qbo from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4qbo] [4qbo_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4QBO: [VRR_NUC ] by SMART
    • Other resources with information on 4QBO
  • Community annotation for 4QBO at PDBWiki (http://pdbwiki.org)

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