1E6G

A-SPECTRIN SH3 DOMAIN A11V, V23L, M25I, V53I, V58L MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Conformational Strain in the Hydrophobic Core and its Implications for Protein Folding and Design

Ventura, S.Vega, M.C.Lacroix, E.Angrand, I.Spagnolo, L.Serrano, L.

(2002) Nat Struct Biol 9: 485

  • DOI: 10.1038/nsb799
  • Primary Citation of Related Structures:  
    1E6G, 1E6H, 1H8K

  • PubMed Abstract: 
  • We have designed de novo 13 divergent spectrin SH3 core sequences to determine their folding properties. Kinetic analysis of the variants with stability similar to that of the wild type protein shows accelerated unfolding and refolding rates compatible with a preferential stabilization of the transition state ...

    We have designed de novo 13 divergent spectrin SH3 core sequences to determine their folding properties. Kinetic analysis of the variants with stability similar to that of the wild type protein shows accelerated unfolding and refolding rates compatible with a preferential stabilization of the transition state. This is most likely caused by conformational strain in the native state, as deletion of a methyl group (Ile-->Val) leads to deceleration in unfolding and increased stability (up to 2 kcal x mol(-1)). Several of these Ile-->Val mutants have negative phi(-U) values, indicating that some noncanonical phi(-U) values might result from conformational strain. Thus, producing a stable protein does not necessarily mean that the design process has been entirely successful. Strained interactions could have been introduced, and a reduction in the buried volume could result in a large increase in stability and a reduction in unfolding rates.


    Related Citations: 
    • Crystal Structure of a Src-Homology 3 (SH3) Domain
      Musacchio, A., Noble, M., Pauptit, R., Wierenga, R., Saraste, M.
      (1992) Nature 359: 851

    Organizational Affiliation

    European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SPECTRIN ALPHA CHAINA62Gallus gallusMutation(s): 5 
Gene Names: SPTAN1SPTA2
UniProt
Find proteins for P07751 (Gallus gallus)
Explore P07751 
Go to UniProtKB:  P07751
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07751
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.267 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.19α = 90
b = 43.52β = 90
c = 53.32γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Advisory, Data collection
  • Version 1.4: 2018-10-24
    Changes: Data collection, Source and taxonomy