4Q7R

Crystal structure of large Stokes shift fluorescent protein LSSmOrange


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Orange Fluorescent Proteins: Structural Studies of LSSmOrange, PSmOrange and PSmOrange2.

Pletnev, S.Shcherbakova, D.M.Subach, O.M.Pletneva, N.V.Malashkevich, V.N.Almo, S.C.Dauter, Z.Verkhusha, V.V.

(2014) Plos One 9: e99136-e99136

  • DOI: 10.1371/journal.pone.0099136
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A structural analysis of the recently developed orange fluorescent proteins with novel phenotypes, LSSmOrange (λex/λem at 437/572 nm), PSmOrange (λex/λem at 548/565 nm and for photoconverted form at 636/662 nm) and PSmOrange2 (λex/λem at 546/561 nm a ...

    A structural analysis of the recently developed orange fluorescent proteins with novel phenotypes, LSSmOrange (λex/λem at 437/572 nm), PSmOrange (λex/λem at 548/565 nm and for photoconverted form at 636/662 nm) and PSmOrange2 (λex/λem at 546/561 nm and for photoconverted form at 619/651 nm), is presented. The obtained crystallographic structures provide an understanding of how the ensemble of a few key mutations enabled special properties of the orange FPs. While only a single Ile161Asp mutation, enabling excited state proton transfer, is critical for LSSmOrange, other substitutions provide refinement of its special properties and an exceptional 120 nm large Stokes shift. Similarly, a single Gln64Leu mutation was sufficient to cause structural changes resulting in photoswitchability of PSmOrange, and only one additional substitution (Phe65Ile), yielding PSmOrange2, was enough to greatly decrease the energy of photoconversion and increase its efficiency of photoswitching. Fluorescence of photoconverted PSmOrange and PSmOrange2 demonstrated an unexpected bathochromic shift relative to the fluorescence of classic red FPs, such as DsRed, eqFP578 and zFP574. The structural changes associated with this fluorescence shift are of considerable value for the design of advanced far-red FPs. For this reason the chromophore transformations accompanying photoconversion of the orange FPs are discussed.


    Organizational Affiliation

    Leidos Biomedical Research Inc., Basic Research Program, Argonne, Illinois, United States of America; Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, Illinois, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LSSmOrange
A, B
245Discosoma sp.Mutation(s): 7 
Find proteins for D0VWW2 (Discosoma sp.)
Go to UniProtKB:  D0VWW2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OFM
Query on OFM
A, B
L-PEPTIDE LINKINGC24 H24 N4 O6PHE, GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.436α = 90.00
b = 107.364β = 102.15
c = 56.602γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SERGUIdata collection
MOLREPphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description