2E21

Crystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus.

• PDB DOI: https://doi.org/10.2210/pdb2E21/pdb

• Classification: LIGASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-11-06 Released: 2007-11-06 
• Deposition Author(s): Kuratani, M., Yoshikawa, Y., Sekine, S., Ishii, T., Shibata, R., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.294 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine

Kuratani, M., Yoshikawa, Y., Bessho, Y., Higashijima, K., Ishii, T., Shibata, R., Takahashi, S., Yutani, K., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 150.57 kDa 
• Atom Count: 10,690 
• Modelled Residue Count: 1,259 
• Deposited Residue Count: 1,268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA(Ile)-lysidine synthase	A, B, C, D	317	Aquifex aeolicus	Mutation(s): 0  Gene Names: tilS EC: 6.3.4 (PDB Primary Data), 6.3.4.19 (UniProt)
UniProt
Find proteins for O67728 (Aquifex aeolicus (strain VF5)) Explore O67728  Go to UniProtKB:  O67728

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	E [auth A], F [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.294 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.456	α = 90
b = 82.231	β = 105.85
c = 109.431	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Kuratani, M., Yoshikawa, Y., Sekine, S., Ishii, T., Shibata, R., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description