3VIC

Green-fluorescent variant of the non-fluorescent chromoprotein Rtms5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A Green Fluorescent Protein Containing a QFG Tri-Peptide Chromophore: Optical Properties and X-Ray Crystal Structure.

Battad, J.M.Traore, D.A.Byres, E.Rossjohn, J.Devenish, R.J.Olsen, S.Wilce, M.C.Prescott, M.

(2012) PLoS One 7: e47331-e47331

  • DOI: https://doi.org/10.1371/journal.pone.0047331
  • Primary Citation of Related Structures:  
    3VIC, 3VK1

  • PubMed Abstract: 

    Rtms5 is an deep blue weakly fluorescent GFP-like protein ([Formula: see text], 592 nm; [Formula: see text], 630nm; Φ(F), 0.004) that contains a (66)Gln-Tyr-Gly chromophore tripeptide sequence. We investigated the optical properties and structure of two variants, Rtms5(Y67F) and Rtms5(Y67F/H146S) in which the tyrosine at position 67 was substituted by a phenylalanine. Compared to the parent proteins the optical spectra for these new variants were significantly blue-shifted. Rtms5(Y67F) spectra were characterised by two absorbing species ([Formula: see text], 440 nm and 513 nm) and green fluorescence emission ([Formula: see text], 440 nm; [Formula: see text], 508 nm; Φ(F), 0.11), whilst Rtms5(Y67F/H146S) spectra were characterised by a single absorbing species ([Formula: see text], 440 nm) and a relatively high fluorescence quantum yield (Φ(F,) 0.75; [Formula: see text], 440 nm; [Formula: see text], 508 nm). The fluorescence emissions of each variant were remarkably stable over a wide range of pH (3-11). These are the first GFP-like proteins with green emissions (500-520 nm) that do not have a tyrosine at position 67. The X-ray crystal structure of each protein was determined to 2.2 Å resolution and showed that the benzylidine ring of the chromophore, similar to the 4-hydroxybenzylidine ring of the Rtms5 parent, is non-coplanar and in the trans conformation. The results of chemical quantum calculations together with the structural data suggested that the 513 nm absorbing species in Rtms5(Y67F) results from an unusual form of the chromophore protonated at the acylimine oxygen. These are the first X-ray crystal structures for fluorescent proteins with a functional chromophore containing a phenylalanine at position 67.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GFP-like non-fluorescent chromoprotein
A, B, C, D, E
A, B, C, D, E, F, G, H
238Montipora efflorescensMutation(s): 1 
UniProt
Find proteins for P83690 (Montipora efflorescens)
Explore P83690 
Go to UniProtKB:  P83690
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83690
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
DA [auth H]
I [auth A]
L [auth B]
O [auth C]
P [auth C]
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
P [auth C],
S [auth D],
T [auth D],
W [auth E]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth G]
CA [auth G]
EA [auth H]
FA [auth H]
AA [auth F],
BA [auth G],
CA [auth G],
EA [auth H],
FA [auth H],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D],
X [auth E],
Y [auth E],
Z [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
QFG
Query on QFG
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC16 H16 N4 O4GLN, PHE, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.271α = 90
b = 186.06β = 90
c = 185.15γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references
  • Version 1.2: 2016-11-02
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations