2DBO | pdb_00002dbo

Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2DBO/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-12-15 Released: 2006-06-15 
• Deposition Author(s): Ishii, T., Shibata, R., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 

Starting Model: experimental

Literature

Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Aquifex aeolicus

Ishii, T., Shibata, R., Bessho, Y., Shirouzu, M., Yokoyama, S.

To be published.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 16.99 kDa 
• Atom Count: 1,228 
• Modeled Residue Count: 148 
• Deposited Residue Count: 148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tyrosyl-tRNA(Tyr) deacylase	A	148	Aquifex aeolicus VF5	Mutation(s): 0  EC: 3.1 (PDB Primary Data), 3.1.1.96 (UniProt)
UniProt
Find proteins for O66742 (Aquifex aeolicus (strain VF5)) Explore O66742  Go to UniProtKB:  O66742

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.01	α = 90
b = 76.01	β = 90
c = 133.754	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-15 
Deposition Author(s): Ishii, T., Shibata, R., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-06-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description