6DQ1

sfGFP N149 mutated to 4-nitro-L-phenylalanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine.

Maurici, N.Savidge, N.Lee, B.U.Brewer, S.H.Phillips-Piro, C.M.

(2018) Acta Crystallogr F Struct Biol Commun 74: 650-655

  • DOI: 10.1107/S2053230X1801169X
  • Primary Citation of Related Structures:  
    6DQ0, 6DQ1

  • PubMed Abstract: 
  • The X-ray crystal structures of two superfolder green fluorescent protein (sfGFP) constructs containing a genetically incorporated spectroscopic reporter unnatural amino acid, 4-nitro-L-phenylalanine (pNO 2 F), at two unique sites in the p ...

    The X-ray crystal structures of two superfolder green fluorescent protein (sfGFP) constructs containing a genetically incorporated spectroscopic reporter unnatural amino acid, 4-nitro-L-phenylalanine (pNO 2 F), at two unique sites in the protein have been determined. Amber codon-suppression methodology was used to site-specifically incorporate pNO 2 F at a solvent-accessible (Asp133) and a partially buried (Asn149) site in sfGFP. The Asp133pNO 2 F sfGFP construct crystallized with two molecules per asymmetric unit in space group P3 2 21 and the crystal structure was refined to 2.05 Å resolution. Crystals of Asn149pNO 2 F sfGFP contained one molecule of sfGFP per asymmetric unit in space group P4 1 22 and the structure was refined to 1.60 Å resolution. The alignment of Asp133pNO 2 F or Asn149pNO 2 F sfGFP with wild-type sfGFP resulted in small root-mean-square deviations, illustrating that these residues do not significantly alter the protein structure and supporting the use of pNO 2 F as an effective spectroscopic reporter of local protein structure and dynamics.


    Organizational Affiliation

    Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
sfGFPA237Aequorea victoriaMutation(s): 0 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
AL-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
PPN
Query on PPN
AL-PEPTIDE LINKINGC9 H10 N2 O4PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.302α = 90
b = 55.302β = 90
c = 166.533γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1053946

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence