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), 0.256 (DCC)
R-Value Work:
0.208 (Depositor)

Starting Model: in silico
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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.247 (Depositor), 0.256 (DCC)
R-Value Work: 0.208 (Depositor)

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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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

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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.