3TRV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/ja210045s
  • Primary Citation of Related Structures:  

  • 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 conta ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-Villin-1
A
35Gallus gallusMutation(s): 1 
Gene Names: VIL1 (VIL)
Find proteins for P02640 (Gallus gallus)
Go to Gene View: VIL1
Go to UniProtKB:  P02640
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-Villin-1
B
35Gallus gallusMutation(s): 1 
Gene Names: VIL1 (VIL)
Find proteins for P02640 (Gallus gallus)
Go to Gene View: VIL1
Go to UniProtKB:  P02640
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  17 Unique
IDChainsTypeFormula2D DiagramParent
DPR
Query on DPR
B
D-PEPTIDE LINKINGC5 H9 N O2

--

PF5
Query on PF5
A
L-PEPTIDE LINKINGC9 H6 F5 N O2PHE
DLY
Query on DLY
B
D-PEPTIDE LINKINGC6 H14 N2 O2

--

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

--

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

--

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

--

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

--

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

--

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

--

DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

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

--

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

--

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

--

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

--

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

--

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

--

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.137 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 20.188α = 75.06
b = 22.390β = 82.00
c = 32.512γ = 87.56
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SHELXDphasing
EMBLdata collection
SCALEPACKdata scaling
XPREPdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-08
    Type: Database references
  • Version 1.2: 2012-02-22
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description