3SDS | pdb_00003sds

Crystal structure of a mitochondrial ornithine carbamoyltransferase from Coccidioides immitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.239 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.193 (Depositor) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Expression of proteins in Escherichia coli as fusions with maltose-binding protein to rescue non-expressed targets in a high-throughput protein-expression and purification pipeline.

Hewitt, S.N.Choi, R.Kelley, A.Crowther, G.J.Napuli, A.J.Van Voorhis, W.C.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1006-1009

  • DOI: https://doi.org/10.1107/S1744309111022159
  • Primary Citation Related Structures: 
    3SDS, 3TL6, 3U40

  • PubMed Abstract: 

    Despite recent advances, the expression of heterologous proteins in Escherichia coli for crystallization remains a nontrivial challenge. The present study investigates the efficacy of maltose-binding protein (MBP) fusion as a general strategy for rescuing the expression of target proteins. From a group of sequence-verified clones with undetectable levels of protein expression in an E. coli T7 expression system, 95 clones representing 16 phylogenetically diverse organisms were selected for recloning into a chimeric expression vector with an N-terminal histidine-tagged MBP. PCR-amplified inserts were annealed into an identical ligation-independent cloning region in an MBP-fusion vector and were analyzed for expression and solubility by high-throughput nickel-affinity binding. This approach yielded detectable expression of 72% of the clones; soluble expression was visible in 62%. However, the solubility of most proteins was marginal to poor upon cleavage of the MBP tag. This study offers large-scale evidence that MBP can improve the soluble expression of previously non-expressing proteins from a variety of eukaryotic and prokaryotic organisms. While the behavior of the cleaved proteins was disappointing, further refinements in MBP tagging may permit the more widespread use of MBP-fusion proteins in crystallographic studies.


  • Organizational Affiliation
    • Seattle Structural Genomics Center for Infectious Disease (SSGCID), University of Washington, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 115.25 kDa 
  • Atom Count: 6,998 
  • Modeled Residue Count: 944 
  • Deposited Residue Count: 1,059 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ornithine carbamoyltransferase, mitochondrial
A, B, C
353Coccidioides immitis RSMutation(s): 0 
Gene Names: CIMG_04084
EC: 2.1.3.3
UniProt
Find proteins for P0CL21 (Coccidioides immitis (strain RS))
Explore P0CL21 
Go to UniProtKB:  P0CL21
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CL21
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.239 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.193 (Depositor) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.36α = 90
b = 150.36β = 90
c = 92.11γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations