3TRY

Crystal structure of racemic villin headpiece subdomain in space group I-4c2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Quasiracemic crystallization as a tool to assess the accommodation of noncanonical residues in nativelike protein conformations.

Mortenson, D.E.Satyshur, K.A.Guzei, I.A.Forest, K.T.Gellman, S.H.

(2012) J Am Chem Soc 134: 2473-2476

  • DOI: https://doi.org/10.1021/ja210045s
  • Primary Citation of Related Structures:  
    3TJW, 3TRV, 3TRW, 3TRY

  • PubMed Abstract: 

    Quasiracemic crystallization has been used to obtain high-resolution structures of two variants of the villin headpiece subdomain (VHP) that contain a pentafluorophenylalanine (F(5)Phe) residue in the hydrophobic core. In each case, the crystal contained the variant constructed from l-amino acids and the native sequence constructed from d-amino acids. We were motivated to undertake these studies by reports that racemic proteins crystallize more readily than homochiral forms and the prospect that quasiracemic crystallization would enable us to determine whether a polypeptide containing a noncanonical residue can closely mimic the tertiary structure of the native sequence. The results suggest that quasiracemic crystallization may prove to be generally useful for assessing mimicry of naturally evolved protein folding patterns by polypeptides that contain unnatural side-chain or backbone subunits.


  • Organizational Affiliation

    Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-Villin-135Gallus gallusMutation(s): 1 
UniProt
Find proteins for P02640 (Gallus gallus)
Explore P02640 
Go to UniProtKB:  P02640
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02640
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: I -4 c 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.128α = 90
b = 63.128β = 90
c = 39.135γ = 90
Software Package:
Software NamePurpose
SAINTdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
SAINTdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-08
    Changes: Database references
  • Version 1.2: 2012-02-22
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection
  • Version 1.5: 2024-10-30
    Changes: Structure summary