3K79 | pdb_00003k79

C38A, C52V Cysteine-Free Variant of Rop (Rom)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3K79

This is version 1.3 of the entry. See complete history

Literature

Cysteine-free Rop: a four-helix bundle core mutant has wild-type stability and structure but dramatically different unfolding kinetics.

Hari, S.B.Byeon, C.Lavinder, J.J.Magliery, T.J.

(2010) Protein Sci 19: 670-679

  • DOI: https://doi.org/10.1002/pro.342
  • Primary Citation Related Structures: 
    3K79

  • PubMed Abstract: 

    Cysteine residues can complicate the folding and storage of proteins due to improper formation of disulfide bonds or oxidation of residues that are natively reduced. Wild-type Rop is a homodimeric four-helix bundle protein and an important model for protein design in the understanding of protein stability, structure and folding kinetics. In the native state, Rop has two buried, reduced cysteine residues in its core, but these are prone to oxidation in destabilized variants, particularly upon extended storage. To circumvent this problem, we designed and characterized a Cys-free variant of Rop, including solving the 2.3 A X-ray crystal structure. We show that the C38A C52V variant has similar structure, stability and in vivo activity to wild-type Rop, but that it has dramatically faster unfolding kinetics like virtually every other mutant of Rop that has been characterized. This cysteine-free Rop has already proven useful for studies on solution topology and on the relationship of core mutations to stability. It also suggests a general strategy for removal of pairs of Cys residues in proteins, both to make them more experimentally tractable and to improve their storage properties for therapeutic or industrial purposes.


  • Organizational Affiliation
    • Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.

Macromolecule Content 

  • Total Structure Weight: 7.13 kDa 
  • Atom Count: 523 
  • Modeled Residue Count: 57 
  • Deposited Residue Count: 63 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Regulatory protein rop63Escherichia coliMutation(s): 2 
Gene Names: rop
UniProt
Find proteins for P03051 (Escherichia coli)
Explore P03051 
Go to UniProtKB:  P03051
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03051
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.664α = 90
b = 40.304β = 101.97
c = 31.666γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description