2O5U

Crystal structure of the PA5185 protein from Pseudomonas Aeruginosa strain PAO1- orthorhombic form (C222).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1.

Chruszcz, M.Zimmerman, M.D.Wang, S.Koclega, K.D.Zheng, H.Evdokimova, E.Kudritska, M.Cymborowski, M.Savchenko, A.Edwards, A.Minor, W.

(2008) Cryst Growth Des 8: 4054-4061

  • DOI: https://doi.org/10.1021/cg800430f
  • Primary Citation of Related Structures:  
    2AV9, 2O5U, 2O6B, 2O6T, 2O6U

  • PubMed Abstract: 

    The crystal structure of PA5185, a putative thioesterase from Pseudomonas aeruginosa strain PAO1, was solved using multi-wavelength anomalous diffraction to 2.4 Å. Analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. The crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative PA5185 substrate (CoA or its derivative). Using new crystallization conditions containing this function-biased set of additives, several new crystal forms were produced and structures of three of them (in three different space groups) were determined. One of the new crystal forms had an improved resolution limit of 1.9 Å, and another displayed an alternative conformation of the highly-conserved loop containing Asn26, which could play a physiological role. Surprisingly, none of the additives were ordered in the crystal structures. Application of function-biased additives could be used as a standard optimization protocol for producing improved diffraction, or new crystal forms, which may lead to better understanding of the biological functions of proteins.


  • Organizational Affiliation

    Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioesterase
A, B, C
148Pseudomonas aeruginosaMutation(s): 0 
Gene Names: PA5185
UniProt
Find proteins for Q9HU04 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HU04 
Go to UniProtKB:  Q9HU04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HU04
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.039α = 90
b = 148.157β = 90
c = 58.328γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2022-04-13
    Changes: Database references, Structure summary
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description