1JML

Conversion of Monomeric Protein L to an Obligate Dimer by Computational Protein Design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Conversion of monomeric protein L to an obligate dimer by computational protein design.

Kuhlman, B.O'Neill, J.W.Kim, D.E.Zhang, K.Y.Baker, D.

(2001) Proc Natl Acad Sci U S A 98: 10687-10691

  • DOI: 10.1073/pnas.181354398
  • Primary Citation of Related Structures:  
    1JML

  • PubMed Abstract: 
  • Protein L consists of a single alpha-helix packed on a four-stranded beta-sheet formed by two symmetrically opposed beta-hairpins. We use a computer-based protein design procedure to stabilize a domain-swapped dimer of protein L in which the second b ...

    Protein L consists of a single alpha-helix packed on a four-stranded beta-sheet formed by two symmetrically opposed beta-hairpins. We use a computer-based protein design procedure to stabilize a domain-swapped dimer of protein L in which the second beta-turn straightens and the C-terminal strand inserts into the beta-sheet of the partner. The designed obligate dimer contains three mutations (A52V, N53P, and G55A) and has a dissociation constant of approximately 700 pM, which is comparable to the dissociation constant of many naturally occurring protein dimers. The structure of the dimer has been determined by x-ray crystallography and is close to the in silico model.


    Organizational Affiliation

    Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LA72Finegoldia magna ATCC 29328Mutation(s): 4 
Find proteins for Q51912 (Finegoldia magna)
Explore Q51912 
Go to UniProtKB:  Q51912
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.762α = 90
b = 76.744β = 90
c = 59.797γ = 90
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2017-10-04
    Changes: Refinement description