3DEE

CRYSTAL STRUCTURE OF A PUTATIVE REGULATORY PROTEIN INVOLVED IN TRANSCRIPTION (NGO1945) FROM NEISSERIA GONORRHOEAE FA 1090 AT 2.25 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.

Das, D.Grishin, N.V.Kumar, A.Carlton, D.Bakolitsa, C.Miller, M.D.Abdubek, P.Astakhova, T.Axelrod, H.L.Burra, P.Chen, C.Chiu, H.J.Chiu, M.Clayton, T.Deller, M.C.Duan, L.Ellrott, K.Ernst, D.Farr, C.L.Feuerhelm, J.Grzechnik, A.Grzechnik, S.K.Grant, J.C.Han, G.W.Jaroszewski, L.Jin, K.K.Johnson, H.A.Klock, H.E.Knuth, M.W.Kozbial, P.Krishna, S.S.Marciano, D.McMullan, D.Morse, A.T.Nigoghossian, E.Nopakun, A.Okach, L.Oommachen, S.Paulsen, J.Puckett, C.Reyes, R.Rife, C.L.Sefcovic, N.Tien, H.J.Trame, C.B.van den Bedem, H.Weekes, D.Wooten, T.Xu, Q.Hodgson, K.O.Wooley, J.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1174-1181

  • DOI: https://doi.org/10.1107/S1744309109022672
  • Primary Citation of Related Structures:  
    3DEE

  • PubMed Abstract: 

    Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (∼40-99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.


  • Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative regulatory protein249Neisseria gonorrhoeae FA 1090Mutation(s): 0 
Gene Names: YP_208969.1NGO1945
UniProt
Find proteins for Q5F5I0 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5F5I0 
Go to UniProtKB:  Q5F5I0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5F5I0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.522α = 90
b = 31.879β = 115.8
c = 86.369γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations