6PQH | pdb_00006pqh

Crystal structure of Asparagine-tRNA ligase from Elizabethkingia sp. CCUG 26117

• PDB DOI: https://doi.org/10.2210/pdb6PQH/pdb

• Classification: LIGASE
• Organism(s): Elizabethkingia sp.
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-07-09 Released: 2019-07-31 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Asparagine-tRNA ligase from Elizabethkingia sp. CCUG 26117

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 226.94 kDa 
• Atom Count: 16,472 
• Modeled Residue Count: 1,899 
• Deposited Residue Count: 1,960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asparagine--tRNA ligase	A, B, C, D	490	Elizabethkingia sp.	Mutation(s): 0  Gene Names: asnS EC: 6.1.1.22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36pqh

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.4	α = 90
b = 110.75	β = 97.09
c = 137.18	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	model building
Coot	model building
BUCCANEER	model building
MR-Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description