1T6H

Crystal Structure T4 Lysozyme incorporating an unnatural amino acid p-iodo-L-phenylalanine at position 153


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The site-specific incorporation of p-iodo-L-phenylalanine into proteins for structure determination.

Xie, J.Wang, L.Wu, N.Brock, A.Spraggon, G.Schultz, P.G.

(2004) Nat Biotechnol 22: 1297-1301

  • DOI: 10.1038/nbt1013
  • Primary Citation of Related Structures:  
    1T6H

  • PubMed Abstract: 
  • A recently developed method makes it possible to genetically encode unnatural amino acids with diverse physical, chemical or biological properties in Escherichia coli and yeast. We now show that this technology can be used to efficiently and site-spe ...

    A recently developed method makes it possible to genetically encode unnatural amino acids with diverse physical, chemical or biological properties in Escherichia coli and yeast. We now show that this technology can be used to efficiently and site-specifically incorporate p-iodo-L-phenylalanine (iodoPhe) into proteins in response to an amber TAG codon. The selective introduction of the anomalously scattering iodine atom into proteins should facilitate single-wavelength anomalous dispersion experiments on in-house X-ray sources. To illustrate this, we generated a Phe153 --> iodoPhe mutant of bacteriophage T4 lysozyme and determined its crystal structure using considerably less data than are needed for the equivalent experiment with cysteine and methionine. The iodoPhe residue, although present in the hydrophobic core of the protein, did not perturb the protein structure in any meaningful way. The ability to selectively introduce this and other heavy atom-containing amino acids into proteins should facilitate the structural study of proteins.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LysozymeA164Escherichia virus T4Mutation(s): 1 
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME

Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHI
Query on PHI
AL-PEPTIDE LINKINGC9 H10 I N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.668α = 90
b = 59.668β = 90
c = 97.574γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-14
    Changes: Experimental preparation