6N0W | pdb_00006n0w

Crystal structure of a Tyrosine--tRNA ligase from Elizabethkingia anophelis

• PDB DOI: https://doi.org/10.2210/pdb6N0W/pdb

• Classification: LIGASE
• Organism(s): Elizabethkingia anophelis NUHP1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-07 Released: 2018-12-05 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a Tyrosine--tRNA ligase from Elizabethkingia anophelis

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.55 kDa 
• Atom Count: 2,762 
• Modeled Residue Count: 364 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase	A	480	Elizabethkingia anophelis NUHP1	Mutation(s): 0  Gene Names: tyrS, BD94_1246 EC: 6.1.1.1
UniProt
Find proteins for A0A077EBU6 (Elizabethkingia anophelis NUHP1) Explore A0A077EBU6  Go to UniProtKB:  A0A077EBU6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36n0w

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.29	α = 90
b = 37.56	β = 112.4
c = 81.76	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Data collection
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description