2PFS

Crystal structure of universal stress protein from Nitrosomonas europaea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural and functional insight into the universal stress protein family.

Tkaczuk, K.L.Shumilin, I.A.Chruszcz, M.Evdokimova, E.Savchenko, A.Minor, W.

(2013) Evol Appl 6: 434-449

  • DOI: 10.1111/eva.12057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We present the crystal structures of two universal stress proteins (USP) from Archaeoglobus fulgidus and Nitrosomonas europaea in both apo- and ligand-bound forms. This work is the first complete synthesis of the structural properties of 26 USP avail ...

    We present the crystal structures of two universal stress proteins (USP) from Archaeoglobus fulgidus and Nitrosomonas europaea in both apo- and ligand-bound forms. This work is the first complete synthesis of the structural properties of 26 USP available in the Protein Data Bank, over 75% of which were determined by structure genomics centers with no additional information provided. The results of bioinformatic analyses of all available USP structures and their sequence homologs revealed that these two new USP structures share overall structural similarity with structures of USPs previously determined. Clustering and cladogram analyses, however, show how they diverge from other members of the USP superfamily and show greater similarity to USPs from organisms inhabiting extreme environments. We compared them with other archaeal and bacterial USPs and discuss their similarities and differences in context of structure, sequential motifs, and potential function. We also attempted to group all analyzed USPs into families, so that assignment of the potential function to those with no experimental data available would be possible by extrapolation.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia Charlottesville, VA, USA ; Midwest Center for Structural Genomics USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Universal stress protein
A
150Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)Mutation(s): 0 
Find proteins for Q82VN8 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Go to UniProtKB:  Q82VN8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.000α = 90.00
b = 76.000β = 90.00
c = 42.987γ = 120.00
Software Package:
Software NamePurpose
DMphasing
HKL-2000data collection
SHELXDphasing
REFMACrefinement
MLPHAREphasing
HKL-2000data scaling
Cootmodel building
RESOLVEphasing
HKL-3000phasing
SHELXEmodel building
ARP/wARPmodel building
HKL-2000data reduction
CCP4phasing
Omodel building
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2011-09-14
    Type: Derived calculations
  • Version 1.4: 2013-04-17
    Type: Database references
  • Version 1.5: 2013-06-26
    Type: Database references