3A05 | pdb_00003a05

Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1 complex with tryptophan

• PDB DOI: https://doi.org/10.2210/pdb3A05/pdb

• Classification: LIGASE
• Organism(s): Aeropyrum pernix
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-02 Released: 2010-03-09 
• Deposition Author(s): Tsuchiya, W., Fujimoto, Z., Hasegawa, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.244 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1

Tsuchiya, W., Fujimoto, Z., Hasegawa, T.

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)

Macromolecule Content 

• Total Structure Weight: 43.11 kDa 
• Atom Count: 3,203 
• Modeled Residue Count: 367 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A	372	Aeropyrum pernix	Mutation(s): 0  Gene Names: trpS, APE_2461.1 EC: 6.1.1.2
UniProt
Find proteins for Q9Y924 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y924  Go to UniProtKB:  Q9Y924

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
TRP	B [auth A]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
CD	D [auth A], E [auth A], F [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.244 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.212	α = 90
b = 102.919	β = 90
c = 97.645	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Tsuchiya, W., Fujimoto, Z., Hasegawa, T.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description