2A5Z

Crystal Structure of Protein of Unknown Function SO2946 from Shewanella oneidensis MR-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.015 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of SO2946 orphan from Shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module.

Nocek, B.Bigelow, L.Abdullah, J.Joachimiak, A.

(2008) J.STRUCT.FUNCT.GENOM. 9: 1-6

  • DOI: 10.1007/s10969-008-9040-0

  • PubMed Abstract: 
  • The crystal structure of the uncharacterized protein SO2946 from Shewanella oneidensis MR-1 was determined with single-wavelength anomalous diffraction (SAD) and refined to 2.0 A resolution. The SO2946 protein consists of a short helical N-terminal d ...

    The crystal structure of the uncharacterized protein SO2946 from Shewanella oneidensis MR-1 was determined with single-wavelength anomalous diffraction (SAD) and refined to 2.0 A resolution. The SO2946 protein consists of a short helical N-terminal domain and a large C-terminal domain with the "jelly-roll" topology. The protein assembles into a propeller consisting of three C-terminal blades arranged around a central core formed by the N-terminal domains. The function of SO2946 could not be inferred from the sequence since the protein represents an orphan with no sequence homologs, but the protein's structure bears a fold similar to that of proteins containing carbohydrate-binding modules. Features such as fold conservation, the presence of a conserved groove and a metal binding region are indicative that SO2946 may be an enzyme and could be involved in binding carbohydrate molecules.


    Organizational Affiliation

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical protein SO2946
A, B, C
262Shewanella oneidensis (strain MR-1)Mutation(s): 0 
Find proteins for Q8ED25 (Shewanella oneidensis (strain MR-1))
Go to UniProtKB:  Q8ED25
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.015 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.590α = 90.00
b = 53.076β = 95.66
c = 112.652γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXCDphasing
SOLVEphasing
SBC-Collectdata collection
REFMACrefinement
HKL-2000data scaling
RESOLVEphasing
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2014-11-19
    Type: Other
  • Version 1.4: 2017-10-11
    Type: Refinement description