8H26 | pdb_00008h26

Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A)

PDB DOI: https://doi.org/10.2210/pdb8H26/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-05 Released: 2023-01-18
Deposition Author(s): Kim, J., Cho, G., Lee, J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.219 (Depositor), 0.225 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A)

Kim, J., Cho, G., Lee, J.

To be published.

Macromolecule Content

Total Structure Weight: 133.33 kDa
Atom Count: 9,201
Modeled Residue Count: 1,046
Deposited Residue Count: 1,170
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16S rRNA (Cytosine(1402)-N(4))-methyltransferase	A, B, C, D, E A, B, C, D, E, F	195	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0 Gene Names: SAOUHSC_01878 EC: 2.1.1.61
UniProt
Find proteins for Q2FXG9 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXG9 Go to UniProtKB: Q2FXG9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FXG9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D]	G [auth A], H [auth B], I [auth C], J [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.219 (Depositor), 0.225 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.329	α = 91.25
b = 69.362	β = 112.97
c = 74.608	γ = 114.05

Software Package:

Software Name	Purpose
REFMAC	refinement
MxDC	data collection
XDS	data reduction
STARANISO	data scaling
Coot	model building
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection
Version 1.2: 2025-12-10
Changes: Data collection, Structure summary

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.