5V0I

Crystal Structure of Tryptophanyl-tRNA Synthetase from Escherichia coli Complexed with AMP and Tryptophan

• PDB DOI: https://doi.org/10.2210/pdb5V0I/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli O157:H7 str. EDL933
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-28 Released: 2017-03-22 
• Deposition Author(s): Maltseva, N., Kim, Y., Mulligan, R., Grimshaw, S.G., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.217 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Crystal Structure of Tryptophanyl-tRNA Synthetase from Escherichia coli Complexed with AMP and Tryptophan

Maltseva, N., Kim, Y., Mulligan, R., Grimshaw, S.G., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 76.77 kDa 
• Atom Count: 5,462 
• Modelled Residue Count: 646 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan--tRNA ligase	A, B	337	Escherichia coli O157:H7 str. EDL933	Mutation(s): 0  Gene Names: trpS, Z4737, ECs4226 EC: 6.1.1.2
UniProt
Find proteins for P67589 (Escherichia coli O157:H7) Explore P67589  Go to UniProtKB:  P67589

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], G [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
TRP	D [auth A], H [auth B]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
FMT	E [auth A], F [auth A], I [auth B], J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.217 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.745	α = 90
b = 110.807	β = 90
c = 128.599	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Maltseva, N., Kim, Y., Mulligan, R., Grimshaw, S.G., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description