4EMQ

Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa.

Nguyen Bich, N.Moeyaert, B.Van Hecke, K.Dedecker, P.Mizuno, H.Hofkens, J.Van Meervelt, L.

(2012) Acta Crystallogr.,Sect.D 68: 1653-1659

  • DOI: 10.1107/S0907444912039686

  • PubMed Abstract: 
  • The crystal structure of the on-state of PDM1-4, a single-mutation variant of the photochromic fluorescent protein Dronpa, is reported at 1.95 Å resolution. PDM1-4 is a Dronpa variant that possesses a slower off-switching rate than Dronpa and thus ca ...

    The crystal structure of the on-state of PDM1-4, a single-mutation variant of the photochromic fluorescent protein Dronpa, is reported at 1.95 Å resolution. PDM1-4 is a Dronpa variant that possesses a slower off-switching rate than Dronpa and thus can effectively increase the image resolution in subdiffraction optical microscopy, although the precise molecular basis for this change has not been elucidated. This work shows that the Lys145Asn mutation in PDM1-4 stabilizes the interface available for dimerization, facilitating oligomerization of the protein. No significant changes were observed in the chromophore environment of PDM1-4 compared with Dronpa, and the ensemble absorption and emission properties of PDM1-4 were highly similar to those of Dronpa. It is proposed that the slower off-switching rate in PDM1-4 is caused by a decrease in the potential flexibility of certain β-strands caused by oligomerization along the AC interface.


    Organizational Affiliation

    Biomolecular Architecture, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven (Heverlee), Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fluorescent protein Dronpa
A, B, C, D, E, F
257Echinophyllia sp. SC22Mutation(s): 1 
Gene Names: Dronpa
Find proteins for Q5TLG6 (Echinophyllia sp. SC22)
Go to UniProtKB:  Q5TLG6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B, C, D, E, F
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B, C, D, E, F
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GYC
Query on GYC
A, B, C, D, E, F
L-PEPTIDE LINKINGC14 H15 N3 O4 SCYS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.539α = 90.00
b = 103.804β = 90.00
c = 177.255γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata scaling
XDSdata reduction
PHENIXrefinement
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references