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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.268 (Depositor), 0.267 (DCC)
R-Value Work:
0.220 (Depositor), 0.223 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: 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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11875
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.268 (Depositor), 0.267 (DCC)
R-Value Work: 0.220 (Depositor), 0.223 (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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.