9EJN | pdb_00009ejn

Crystal structure of magnesium-transporting ATPase MgtA in an E1-like magnesium-bound state

PDB DOI: https://doi.org/10.2210/pdb9EJN/pdb

Classification: METAL TRANSPORT
Organism(s): Lactococcus lactis subsp. lactis CV56
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2024-11-28 Released: 2025-02-26
Deposition Author(s): Khan, M.B., Primeau, J.O., Basu, P.C., Morth, J.P., Lemieux, M.J., Young, H.S.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.55 Å
R-Value Free:
0.339 (Depositor), 0.344 (DCC)
R-Value Work:
0.288 (Depositor), 0.293 (DCC)
R-Value Observed:
0.290 (Depositor)

Starting Model: in silico
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of magnesium-transporting ATPase MgtA in an E1-like magnesium-bound state

Khan, M.B., Primeau, J.O., Basu, P.C., Morth, J.P., Lemieux, M.J., Young, H.S.

To be published.

Macromolecule Content

Total Structure Weight: 406.11 kDa
Atom Count: 27,352
Modeled Residue Count: 3,556
Deposited Residue Count: 3,684
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium-transporting ATPase, P-type 1	A, B [auth C], C [auth B], D	921	Lactococcus lactis subsp. lactis CV56	Mutation(s): 0 Gene Names: LL275_1350 EC: 7.2.2.14 Membrane Entity: Yes
UniProt
Find proteins for A0A2X0R2L8 (Lactococcus lactis) Explore A0A2X0R2L8 Go to UniProtKB: A0A2X0R2L8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2X0R2L8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth B] SDF format, chain F [auth C] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth B] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth B] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth C], G [auth B], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth B] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth B] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.55 Å
R-Value Free: 0.339 (Depositor), 0.344 (DCC)
R-Value Work: 0.288 (Depositor), 0.293 (DCC)
R-Value Observed: 0.290 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.403	α = 90
b = 66.595	β = 90.151
c = 218.666	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2025-02-26
Type: Initial release
Version 1.1: 2025-03-05
Changes: Database references, Structure summary

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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.