1YIA | pdb_00001yia

Crystal structure of tryptophanyl tRNA synthetase II from Deinococcus radiodurans in complex with 5-Hydroxy tryptophan.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.290 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.280 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.280 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HRPClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Structure and activity of an aminoacyl-tRNA synthetase that charges tRNA with nitro-tryptophan.

Buddha, M.R.Crane, B.R.

(2005) Nat Struct Mol Biol 12: 274-275

  • DOI: https://doi.org/10.1038/nsmb907
  • Primary Citation of Related Structures:  
    1YI8, 1YIA

  • PubMed Abstract: 

    The most divergent of two tryptophanyl tRNA synthetases (TrpRS II) found in Deinococcus radiodurans interacts with a nitric oxide synthase protein that produces 4-nitro-tryptophan (4-NRP). TrpRS II efficiently charges transfer RNA(Trp) with 4-NRP and 5-hydroxy-tryptophan (5-HRP). The crystal structures of TrpRS II bound to tryptophan and 5-HRP reveal residue substitutions that accommodate modified indoles. A class of auxiliary bacterial TrpRSs conserve this capacity to charge tRNA with nonstandard amino acids.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tryptophanyl-tRNA synthetaseA [auth B],
B [auth A],
C
351Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Gene Names: DR1093
EC: 6.1.1.2
UniProt
Find proteins for Q9RVD6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RVD6 
Go to UniProtKB:  Q9RVD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RVD6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HRP
Query on HRP

Download Ideal Coordinates CCD File 
D [auth B]5-HYDROXY-L-TRYPTOPHAN
C11 H12 N2 O3
LDCYZAJDBXYCGN-SECBINFHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.290 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.280 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.280 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.2α = 90
b = 58.4β = 96.5
c = 86.8γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HRPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Data collection
  • Version 1.4: 2018-02-07
    Changes: Experimental preparation
  • Version 1.5: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations