2RA9

Crystal structure of a duf1285 family protein (sbal_2486) from shewanella baltica os155 at 1.40 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 DUF1285
A
150Shewanella baltica (strain OS155 / ATCC BAA-1091)Mutation(s): 0 
Find proteins for A3D5G6 (Shewanella baltica (strain OS155 / ATCC BAA-1091))
Go to UniProtKB:  A3D5G6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 38.409α = 90.00
b = 62.286β = 90.00
c = 73.247γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
MOSFLMdata reduction
SHARPphasing
SCALAdata scaling
REFMACrefinement
SHELXphasing
MolProbitymodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2012-10-24
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Refinement description