1YI8 | pdb_00001yi8

Crystal structure of tryptophanyl trRNA synthetase II from Deinococcus radiodurans in complex with L-Trp

• PDB DOI: https://doi.org/10.2210/pdb1YI8/pdb

• Classification: LIGASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-11 Released: 2005-02-22 
• Deposition Author(s): Buddha, M.R., Crane, B.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.280 (Depositor), 0.509 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.496 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

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

• PubMed: 15723076 
• DOI: https://doi.org/10.1038/nsmb907
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 114.88 kDa 
• Atom Count: 8,661 
• Modeled Residue Count: 993 
• Deposited Residue Count: 1,053 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tryptophanyl-tRNA synthetase	A [auth B], B [auth A], C	351	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRP	D [auth C]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.280 (Depositor), 0.509 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.496 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.8	α = 90
b = 58.5	β = 100.725
c = 88.9	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
Deposition Author(s): Buddha, M.R., Crane, B.R.

Revision History  

• 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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations