3FEP

Crystal structure of the R132K:R111L:L121E:R59W-CRABPII mutant complexed with a synthetic ligand (merocyanin) at 2.60 angstrom resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

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Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history


Literature

"Turn-on" protein fluorescence: in situ formation of cyanine dyes.

Yapici, I.Lee, K.S.Berbasova, T.Nosrati, M.Jia, X.Vasileiou, C.Wang, W.Santos, E.M.Geiger, J.H.Borhan, B.

(2015) J Am Chem Soc 137: 1073-1080

  • DOI: https://doi.org/10.1021/ja506376j
  • Primary Citation of Related Structures:  
    3FEP, 4QGV, 4QGW, 4QGX

  • PubMed Abstract: 

    Protein reengineering of cellular retinoic acid binding protein II (CRABPII) has yielded a genetically addressable system, capable of binding a profluorophoric chromophore that results in fluorescent protein/chromophore complexes. These complexes exhibit far-red emission, with high quantum efficiencies and brightness and also exhibit excellent pH stability spanning the range of 2-11. In the course of this study, it became evident that single mutations of L121E and R59W were most effective in improving the fluorescent characteristics of CRABPII mutants as well as the kinetics of complex formation. The readily crystallizable nature of these proteins was invaluable to provide clues for the observed spectroscopic behavior that results from single mutation of key residues.


  • Organizational Affiliation

    Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2137Homo sapiensMutation(s): 4 
Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens)
Explore P29373 
Go to UniProtKB:  P29373
PHAROS:  P29373
GTEx:  ENSG00000143320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29373
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMC
Query on LMC

Download Ideal Coordinates CCD File 
B [auth A](2E,4E,6E)-3-methyl-6-(1,3,3-trimethyl-1,3-dihydro-2H-indol-2-ylidene)hexa-2,4-dienal
C18 H21 N O
UGINWNVBXWWHCS-RZZAMGAFSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
C [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.808α = 90
b = 55.808β = 90
c = 108.177γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-02-04
    Changes: Database references
  • Version 1.3: 2015-02-11
    Changes: Database references
  • Version 1.4: 2016-12-28
    Changes: Structure summary
  • Version 1.5: 2020-09-09
    Changes: Derived calculations, Structure summary
  • Version 1.6: 2021-10-20
    Changes: Database references
  • Version 1.7: 2023-09-06
    Changes: Data collection, Refinement description