SCCmec type IV LP1413 - nucleic acids binding protein

Experimental Data Snapshot

  • Resolution: 2.18 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements.

Mir-Sanchis, I.Pigli, Y.Z.Rice, P.A.

(2018) Structure 26: 1144

  • DOI: https://doi.org/10.1016/j.str.2018.05.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Methicillin-resistant Staphylococcus aureus is a global public health threat. Methicillin resistance is carried on mobile genetic elements belonging to the staphylococcal cassette chromosome (SCC) family. The molecular mechanisms that SCC elements exploit for stable maintenance and for horizontal transfer are poorly understood. Previously, we identified several conserved SCC genes with putative functions in DNA replication, including lp1413, which we found encodes a single-stranded DNA (ssDNA)-binding protein. We report here the 2.18 Å crystal structure of LP1413, which shows that it adopts a winged helix-turn-helix fold rather than the OB-fold normally seen in replication-related ssDNA-binding proteins. However, conserved residues form a hydrophobic pocket not normally found in winged helix-turn-helix domains. LP1413 also has a conserved but disordered C-terminal tail. As deletion of the tail does not significantly affect cooperative binding to ssDNA, we propose that it mediates interactions with other proteins. LP1413 could play several different roles in vivo.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57(th) St., Chicago, IL 60637, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LP1413 - SCCmec type IV-encoded DNA binding protein
A, B
96Staphylococcus aureusMutation(s): 0 
Gene Names: CEJ93_14580R114_18R15_21R17_21R92_18R95_21R99_21
Find proteins for Q0WXP5 (Staphylococcus aureus)
Explore Q0WXP5 
Go to UniProtKB:  Q0WXP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0WXP5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.033α = 90
b = 97.033β = 90
c = 127.794γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM121655

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence