3SZ3 | pdb_00003sz3

Crystal structure of Tryptophanyl-tRNA synthetase from Vibrio cholerae with an endogenous tryptophan

• PDB DOI: https://doi.org/10.2210/pdb3SZ3/pdb

• Classification: LIGASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-18 Released: 2011-09-14 
• Deposition Author(s): Cooper, D.R., Kudritska, M., Chruszcz, M., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.179 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Tryptophanyl-tRNA synthetase from Vibrio cholerae with an endogenous tryptophan

Cooper, D.R., Kudritska, M., Chruszcz, M., Grabowski, M., Anderson, W.F., Minor, W.

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: 38.04 kDa 
• Atom Count: 3,231 
• Modeled Residue Count: 341 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A	341	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: trpS, VC_2623 EC: 6.1.1.2
UniProt
Find proteins for Q9KNV7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KNV7  Go to UniProtKB:  Q9KNV7

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
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.179 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m3qc7w

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.02	α = 90
b = 94.047	β = 90
c = 47.036	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-14 
Deposition Author(s): Cooper, D.R., Kudritska, M., Chruszcz, M., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-09-14
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Refinement description