3TRV | pdb_00003trv

Crystal structure of quasiracemic villin headpiece subdomain containing (F5Phe17) substitution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 
    0.155 (Depositor), 0.153 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.135 (DCC) 
  • R-Value Observed: 
    0.138 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 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
L-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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D-Villin-135Gallus gallusMutation(s): 1 
UniProt
Find proteins for P02640 (Gallus gallus)
Explore P02640 
Go to UniProtKB:  P02640
Entity Groups  
UniProt GroupP02640
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  17 Unique
IDChains TypeFormula2D DiagramParent
PF5
Query on PF5
A
L-PEPTIDE LINKINGC9 H6 F5 N O2PHE
DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

DAR
Query on DAR
B
D-PEPTIDE LINKINGC6 H15 N4 O2

--

DAS
Query on DAS
B
D-PEPTIDE LINKINGC4 H7 N O4

--

DGL
Query on DGL
B
D-PEPTIDE LINKINGC5 H9 N O4

--

DGN
Query on DGN
B
D-PEPTIDE LINKINGC5 H10 N2 O3

--

DHI
Query on DHI
B
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DLE
Query on DLE
B
D-PEPTIDE LINKINGC6 H13 N O2

--

DLY
Query on DLY
B
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DPN
Query on DPN
B
D-PEPTIDE LINKINGC9 H11 N O2

--

DPR
Query on DPR
B
D-PEPTIDE LINKINGC5 H9 N O2

--

DSG
Query on DSG
B
D-PEPTIDE LINKINGC4 H8 N2 O3

--

DSN
Query on DSN
B
D-PEPTIDE LINKINGC3 H7 N O3

--

DTH
Query on DTH
B
D-PEPTIDE LINKINGC4 H9 N O3

--

DTR
Query on DTR
B
D-PEPTIDE LINKINGC11 H12 N2 O2

--

DVA
Query on DVA
B
D-PEPTIDE LINKINGC5 H11 N O2

--

MED
Query on MED
B
D-PEPTIDE LINKINGC5 H11 N O2 S

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free:  0.155 (Depositor), 0.153 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.135 (DCC) 
  • R-Value Observed: 0.138 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 20.188α = 75.061
b = 22.39β = 82.004
c = 32.512γ = 87.558
Software Package:
Software NamePurpose
XPREPdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
EMBLdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



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: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary