2RE3

CRYSTAL STRUCTURE OF a DUF1285 family protein (SPO_0140) FROM SILICIBACTER POMEROYI DSS-3 AT 2.50 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.

Han, G.W.Bakolitsa, C.Miller, M.D.Kumar, A.Carlton, D.Najmanovich, R.J.Abdubek, P.Astakhova, T.Axelrod, H.L.Chen, C.Chiu, H.J.Clayton, T.Das, D.Deller, M.C.Duan, L.Ernst, D.Feuerhelm, J.Grant, J.C.Grzechnik, A.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.Okach, L.Reyes, R.Rife, C.L.Sefcovic, N.Tien, H.J.Trame, C.B.van den Bedem, H.Weekes, D.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 66: 1218-1225

  • DOI: 10.1107/S1744309109050416
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of SPO0140 and Sbal_2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a con ...

    The crystal structures of SPO0140 and Sbal_2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, B
194Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)Mutation(s): 0 
Find proteins for Q5LWU5 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Go to UniProtKB:  Q5LWU5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 75.370α = 90.00
b = 75.370β = 90.00
c = 182.687γ = 90.00
Software Package:
Software NamePurpose
MolProbitymodel building
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
SHARPphasing
MAR345data collection
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence, Refinement description