3NL9 Crystal structure of a putative NTP pyrophosphohydrolase (Exig_1061) from EXIGUOBACTERIUM SP. 255-15 at 1.78 A resolution date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.78
ligand EDO, MSE enzyme
note 3NL9 supersedes 3MQU, 2RFP
Gene EXIG
Primary referenceStructure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15., Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1237-44. Epub 2010 Aug 4. PMID:20944217
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (63 Kb) [Save to disk]
  • Biological Unit Coordinates (3nl9.pdb1.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 3NL9
  • CSU: Contacts of Structural Units for 3NL9
  • Structure Factors (1345 Kb)
  • Retrieve 3NL9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NL9 from S2C, [Save to disk]
  • Re-refined 3nl9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NL9 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 3NL9
  • 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 3NL9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nl9] [3nl9_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3NL9
  • Community annotation for 3NL9 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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