3DEE CRYSTAL STRUCTURE OF A PUTATIVE REGULATORY PROTEIN INVOLVED IN TRANSCRIPTION (NGO1945) FROM NEISSERIA GONORRHOEAE FA 1090 AT 2.25 A RESOLUTION date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.10
ligand CL, IMD, MSE enzyme
Gene YP
Primary referenceThe structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation., Das D, Grishin NV, Kumar A, Carlton D, Bakolitsa C, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Burra P, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grzechnik A, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1174-81. Epub 2009 Oct 27. PMID:20944208
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (3dee.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 3DEE
  • CSU: Contacts of Structural Units for 3DEE
  • Likely Quarternary Molecular Structure file(s) for 3DEE
  • Structure Factors (1319 Kb)
  • Retrieve 3DEE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DEE from S2C, [Save to disk]
  • Re-refined 3dee structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DEE 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 3DEE
  • 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 3DEE, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dee_A] [3dee]
  • SWISS-PROT database: [Q5F5I0]
  • Domain organization of [Q5F5I0_NEIG1] by SWISSPFAM
    • Other resources with information on 3DEE
  • Community annotation for 3DEE 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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