5TEW | pdb_00005tew

Crystal structure of a tryptophanyl-tRNA synthetase from Neisseria gonorrhoeae bound to tryptophan

• PDB DOI: https://doi.org/10.2210/pdb5TEW/pdb

• Classification: LIGASE
• Organism(s): Neisseria gonorrhoeae FA 1090
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-22 Released: 2016-10-05 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.263 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a tryptophanyl-tRNA synthetase from Neisseria gonorrhoeae bound to tryptophan

Edwards, T.E., Dranow, D.M., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.96 kDa 
• Atom Count: 2,528 
• Modeled Residue Count: 333 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan--tRNA ligase	A	344	Neisseria gonorrhoeae FA 1090	Mutation(s): 0  Gene Names: trpS, NGO_1045 EC: 6.1.1.2
UniProt
Find proteins for Q5F7X0 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F7X0  Go to UniProtKB:  Q5F7X0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRP	B [auth A]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.263 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35tew

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.94	α = 90
b = 59.94	β = 90
c = 162.93	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2025-10-22
  Changes: Database references, Structure summary