Crystal structure of putative acetyltransferase

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 

Starting Model: experimental
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Genetic Encoding of 3-Iodo-l-Tyrosine in Escherichia coli for Single-Wavelength Anomalous Dispersion Phasing in Protein Crystallography

Sakamoto, K.Murayama, K.Oki, K.Iraha, F.Kato-Murayama, M.Takahashi, M.Ohtake, K.Kobayashi, T.Kuramitsu, S.Shirouzu, M.Yokoyama, S.

(2009) Structure 17: 335-344

  • DOI: https://doi.org/10.1016/j.str.2009.01.008
  • Primary Citation of Related Structures:  
    2Z0Z, 2Z10, 2ZXV

  • PubMed Abstract: 

    We developed an Escherichia coli cell-based system to generate proteins containing 3-iodo-L-tyrosine at desired sites, and we used this system for structure determination by single-wavelength anomalous dispersion (SAD) phasing with the strong iodine signal. Tyrosyl-tRNA synthetase from Methanocaldococcus jannaschii was engineered to specifically recognize 3-iodo-L-tyrosine. The 1.7 A crystal structure of the engineered variant, iodoTyrRS-mj, bound with 3-iodo-L-tyrosine revealed the structural basis underlying the strict specificity for this nonnatural substrate; the iodine moiety makes van der Waals contacts with 5 residues at the binding pocket. E. coli cells expressing iodoTyrRS-mj and the suppressor tRNA were used to incorporate 3-iodo-L-tyrosine site specifically into the ribosomal protein N-acetyltransferase from Thermus thermophilus. The crystal structure of this enzyme with iodotyrosine was determined at 1.8 and 2.2 Angstroms resolutions by SAD phasing at CuK alpha and CrK alpha wavelengths, respectively. The native structure, determined by molecular replacement, revealed no significant structural distortion caused by iodotyrosine incorporation.

  • Organizational Affiliation

    RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein TTHA1799194Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q5SHD1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHD1 
Go to UniProtKB:  Q5SHD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHD1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.468α = 90
b = 71.468β = 90
c = 99.159γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description