9SHC | pdb_00009shc

Structure of Streptococcus pneumoniae methionyl-tRNA synthetase bound to the sulphamoyl analogue of methionyl-adenylate

PDB DOI: https://doi.org/10.2210/pdb9SHC/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-26 Released: 2025-09-24
Deposition Author(s): Cusack, S., Fridd, S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.247 (Depositor), 0.254 (DCC)
R-Value Work:
0.208 (Depositor), 0.216 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of Streptococcus pneumoniae methionyl-tRNA synthetase bound to the sulphamoyl analogue of methionine-adenylate

Cusack, S.

To be published.

Macromolecule Content

Total Structure Weight: 76.21 kDa
Atom Count: 4,129
Modeled Residue Count: 498
Deposited Residue Count: 665
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine--tRNA ligase	A	665	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: metG, metS, SP_0788 EC: 6.1.1.10
UniProt
Find proteins for P67580 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P67580 Go to UniProtKB: P67580
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P67580
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1MAL (Subject of Investigation/LOI) Query on A1MAL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methylsulfanyl-butanoyl]sulfamate C₁₅ H₂₃ N₇ O₇ S₂ PBPVXRRYIIRSNJ-JVEUSOJLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.247 (Depositor), 0.254 (DCC)
R-Value Work: 0.208 (Depositor), 0.216 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.365	α = 90
b = 72.888	β = 117.42
c = 78.881	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	France	--

Revision History (Full details and data files)

Version 1.0: 2025-09-24
Type: Initial release

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.