5YYN | pdb_00005yyn

Crystal structures of E.coli arginyl-trna synthetase (argrs) in complex with substrate TRNA(Arg)

• PDB DOI: https://doi.org/10.2210/pdb5YYN/pdb
• NAKB: 5YYN

• Classification: LIGASE/RNA
• Organism(s): Escherichia coli K-12, Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-10 Released: 2018-12-12 
• Deposition Author(s): Zhou, M., Ye, S., Stephen, P., Zhang, R.G., Wang, E.D., Giege, R., Lin, S.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures Of E.Coli Arginyl-Trna Synthetase (Argrs) In Complex With Substrates

Zhou, M., Ye, S., Stephen, P., Zhang, R.G., Wang, E.D., Giege, R., Lin, S.X.

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 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 181.2 kDa 
• Atom Count: 11,523 
• Modeled Residue Count: 1,243 
• Deposited Residue Count: 1,326 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine--tRNA ligase	A, C	586	Escherichia coli K-12	Mutation(s): 0  Gene Names: argS, b1876, JW1865 EC: 6.1.1.19
UniProt
Find proteins for P11875 (Escherichia coli (strain K12)) Explore P11875  Go to UniProtKB:  P11875

Entity ID: 2
Molecule	Chains	Length	Organism	Image
TRNA	B, D	77	Geobacillus stearothermophilus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.241	α = 90
b = 102.241	β = 90
c = 480.567	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Zhou, M., Ye, S., Stephen, P., Zhang, R.G., Wang, E.D., Giege, R., Lin, S.X.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description