3JXE | pdb_00003jxe

Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase in complex with TrpAMP

• PDB DOI: https://doi.org/10.2210/pdb3JXE/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-19 Released: 2009-11-10 
• Deposition Author(s): Zhou, M., Dong, X., Zhong, C., Shen, N., Yang, B., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.258 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Crystal structure of P. horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase

Zhou, M., Dong, X., Zhong, C., Shen, N., Yang, B., Ding, J.

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: 93.66 kDa 
• Atom Count: 6,131 
• Modeled Residue Count: 724 
• Deposited Residue Count: 784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A, B	392	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH1921, trpS EC: 6.1.1.2
UniProt
Find proteins for O59584 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59584  Go to UniProtKB:  O59584

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYM	C [auth A], E [auth B]	TRYPTOPHANYL-5'AMP C21 H24 N7 O8 P IFQVDHDRFCKAAW-SQIXAUHQSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.258 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.198	α = 90
b = 170.198	β = 90
c = 170.198	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Zhou, M., Dong, X., Zhong, C., Shen, N., Yang, B., Ding, J.

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations