2E89 | pdb_00002e89

Crystal structure of Aquifex aeolicus TilS in a complex with ATP, Magnesium ion, and L-lysine

• PDB DOI: https://doi.org/10.2210/pdb2E89/pdb

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


• Deposited: 2007-01-19 Released: 2007-11-13 
• Deposition Author(s): Kuratani, M., Yoshikawa, Y., Takahashi, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.274 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

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 (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 (software)

Macromolecule Content 

• Total Structure Weight: 151.76 kDa 
• Atom Count: 10,642 
• Modeled Residue Count: 1,258 
• 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  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], G [auth B], I [auth C], J [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
LYS	F [auth B]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
MG	H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.274 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.42	α = 90
b = 81.57	β = 105.98
c = 109.11	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: 2007-11-13 
Deposition Author(s): Kuratani, M., Yoshikawa, Y., Takahashi, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-13
  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
• Version 1.3: 2024-10-09
  Changes: Structure summary