Crystal structure of a protein with unknown function (YP_749275.1) from Shewanella Frigidimarina NCIMB 400 at 1.80 A resolution

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding.

Kumar, A.Lomize, A.Jin, K.K.Carlton, D.Miller, M.D.Jaroszewski, L.Abdubek, P.Astakhova, T.Axelrod, H.L.Chiu, H.J.Clayton, T.Das, D.Deller, M.C.Duan, L.Feuerhelm, J.Grant, J.C.Grzechnik, A.Han, G.W.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 Struct Biol Cryst Commun 66: 1245-1253

  • DOI: https://doi.org/10.1107/S1744309109042481
  • Primary Citation of Related Structures:  
    2OOK, 2Q3L

  • PubMed Abstract: 

    The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica, respectively, have been determined at 1.8 and 2.25 Å resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the α/β SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their α2 and α3 helices. In the `open' conformation (YP_001095227.1), these helices are 15 Å apart, leading to the creation of a deep nonpolar cavity. In the `closed' structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic surface. These two complementary structures are reminiscent of the conformational switch in CRAL-TRIO carriers of hydrophobic compounds. It is suggested that both proteins may associate with the lipid bilayer in their `open' monomeric state by inserting their amphiphilic helices, α2 and α3, into the lipid bilayer. These bacterial proteins may function as carriers of nonpolar substances or as interfacially activated enzymes.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein
A, B
127Shewanella frigidimarina NCIMB 400Mutation(s): 3 
Gene Names: YP_749275.1Sfri_0576
Find proteins for Q087X8 (Shewanella frigidimarina (strain NCIMB 400))
Explore Q087X8 
Go to UniProtKB:  Q087X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ087X8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.579α = 90
b = 40.412β = 92.23
c = 78.05γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-01-25
    Changes: Database references, Derived calculations