5YYM

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.

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11875
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARG (Subject of Investigation/LOI) Query on ARG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.