4TYM Transferase date Jul 08, 2014
title Crystal Structure Of Purine Nucleoside Phosphorylase From Streptococcus Agalactiae 2603vr, Nysgrc Target 030935
authors V.N.Malashkevich, R.Bhosle, R.Toro, B.Hillerich, A.Gizzi, S.Garfo A.Kar, M.K.Chan, J.Lafluer, H.Patel, B.Matikainen, S.Chamala, S.L A.Celikgil, G.Villegas, B.Evans, J.Love, A.Fiser, R.Seidel, J.B.B S.C.Almo, New York Structural Genomics Research Consortium (
compound source
Molecule: Purine Nucleoside Phosphorylase Deod-Type
Chain: A
Synonym: Pnp
Engineered: Yes
Organism_scientific: Streptococcus Agalactiae Lmg 15084
Organism_taxid: 1105274
Gene: Deod, Sag0083_03075
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Codon+Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Bc-Psgx3(Bc)
symmetry Space Group: P 63 2 2
R_factor 0.166 R_Free 0.193
length a length b length c angle alpha angle beta angle gamma
156.552 156.552 52.090 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand CSO, MSE, SO4 enzyme Transferase E.C. BRENDA
Gene SAG0083

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (4tym.pdb1.gz) 80 Kb
  • Biological Unit Coordinates (4tym.pdb2.gz) 472 Kb
  • LPC: Ligand-Protein Contacts for 4TYM
  • CSU: Contacts of Structural Units for 4TYM
  • Structure Factors (972 Kb)
  • Retrieve 4TYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4TYM from S2C, [Save to disk]
  • Re-refined 4tym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4TYM 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 4TYM
  • 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 4TYM, from MSDmotif at EBI
  • Fold representative 4tym from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4tym_A] [4tym]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4TYM
  • Community annotation for 4TYM at PDBWiki (http://pdbwiki.org)

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