3N9I | pdb_00003n9i

Crystal structure of tryptophanyl-tRNA synthetase from Yersinia pestis CO92

• PDB DOI: https://doi.org/10.2210/pdb3N9I/pdb

• Classification: LIGASE
• Organism(s): Yersinia pestis CO92
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2010-05-30 Released: 2010-07-21 
• Deposition Author(s): Nocek, B., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tryptophanyl-tRNA synthetase from Yersinia pestis CO92

Nocek, B., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., 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: 77.56 kDa 
• Atom Count: 5,685 
• Modeled Residue Count: 664 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A, B	346	Yersinia pestis CO92	Mutation(s): 0  Gene Names: trpS, YPO0157, y3940, YP_0159 EC: 6.1.1.2
UniProt
Find proteins for Q8ZJF2 (Yersinia pestis) Explore Q8ZJF2  Go to UniProtKB:  Q8ZJF2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33n9i

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.099	α = 90
b = 78.15	β = 90
c = 152.176	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Nocek, B., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-10-01
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description