2YF3 Hydrolase date Apr 01, 2011
title Crystal Structure Of Dr2231, The Mazg-Like Protein From Dein Radiodurans, Complex With Manganese
authors A.M.D.Goncalves, D.Desanctis, S.M.Mcsweeney
compound source
Molecule: Mazg-Like Nucleoside Triphosphate Pyrophosphohydr
Chain: A, B, C, D, E, F
Ec: 3.6.1.19
Engineered: Yes
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 243230
Strain: R1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet151d-Topo
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.109 111.402 166.539 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand GOL, MN, SO4 enzyme Hydrolase E.C.3.6.1.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructural and Functional Insights into DR2231 Protein, the MazG-like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus radiodurans., Goncalves AM, de Sanctis D, McSweeney SM, J Biol Chem. 2011 Sep 2;286(35):30691-705. Epub 2011 Jul 6. PMID:21733847
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (458 Kb) [Save to disk]
  • Biological Unit Coordinates (2yf3.pdb1.gz) 149 Kb
  • Biological Unit Coordinates (2yf3.pdb2.gz) 155 Kb
  • Biological Unit Coordinates (2yf3.pdb3.gz) 150 Kb
  • LPC: Ligand-Protein Contacts for 2YF3
  • CSU: Contacts of Structural Units for 2YF3
  • Structure Factors (4553 Kb)
  • Retrieve 2YF3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YF3 from S2C, [Save to disk]
  • Re-refined 2yf3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YF3 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 2YF3
  • 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 2YF3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yf3_D] [2yf3_E] [2yf3_B] [2yf3] [2yf3_F] [2yf3_A] [2yf3_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2YF3
  • Community annotation for 2YF3 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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