5YYM | pdb_00005yym

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

• PDB DOI: https://doi.org/10.2210/pdb5YYM/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• 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: 2.20 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 131.9 kDa 
• Atom Count: 9,608 
• Modeled Residue Count: 1,154 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine--tRNA ligase	A, B	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG (Subject of Investigation/LOI)	C [auth A], D [auth B]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.727	α = 90
b = 244.51	β = 90.69
c = 52.46	γ = 90

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