6YLP | pdb_00006ylp

EGFP_in_Acidic_env Directionality of Optical Properties of Fluorescent Proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.207 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6YLP

This is version 2.2 of the entry. See complete history

Literature

Directionality of light absorption and emission in representative fluorescent proteins.

Myskova, J.Rybakova, O.Brynda, J.Khoroshyy, P.Bondar, A.Lazar, J.

(2020) Proc Natl Acad Sci U S A 117: 32395-32401

  • DOI: https://doi.org/10.1073/pnas.2017379117
  • Primary Citation Related Structures: 
    6YLM, 6YLN, 6YLO, 6YLP, 6YLQ, 6YLS

  • PubMed Abstract: 

    Fluorescent molecules are like antennas: The rate at which they absorb light depends on their orientation with respect to the incoming light wave, and the apparent intensity of their emission depends on their orientation with respect to the observer. However, the directions along which the most important fluorescent molecules in biology, fluorescent proteins (FPs), absorb and emit light are generally not known. Our optical and X-ray investigations of FP crystals have now allowed us to determine the molecular orientations of the excitation and emission transition dipole moments in the FPs mTurquoise2, eGFP, and mCherry, and the photoconvertible FP mEos4b. Our results will allow using FP directionality in studies of molecular and biological processes, but also in development of novel bioengineering and bioelectronics applications.


  • Organizational Affiliation
    • Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 28.65 kDa 
  • Atom Count: 1,992 
  • Modeled Residue Count: 227 
  • Deposited Residue Count: 250 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
eGFP_in_Acidic_env250synthetic constructMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GYS
Query on GYS
A
L-PEPTIDE LINKINGC14 H15 N3 O5SER, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.207 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.97α = 90
b = 62.15β = 90
c = 68.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.02.1.01/0.0/0.0/16_019/0000729

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-01-24
    Changes: Refinement description
  • Version 2.2: 2024-10-23
    Changes: Structure summary