7UUM | pdb_00007uum

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with paromomycin and coenzyme A

PDB DOI: https://doi.org/10.2210/pdb7UUM/pdb

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

Deposited: 2022-04-28 Released: 2022-11-02
Deposition Author(s): Stogios, P.J., Evdokimova, E., Osipiuk, J., Di Leo, R., Bordeleau, E., Wright, G.D., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.223 (Depositor), 0.223 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance

Bordeleau, E., Stogios, P.J., Evdokimova, E., Koteva, K., Savchenko, A., Wright, G.D.

(2024) Nat Chem Biol 20: 234-242

DOI: https://doi.org/10.1038/s41589-023-01483-3

Macromolecule Content

Total Structure Weight: 32.8 kDa
Atom Count: 2,344
Modeled Residue Count: 274
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminocyclitol acetyltransferase ApmA	A	276	Staphylococcus aureus	Mutation(s): 0 Gene Names: apmA
UniProt
Find proteins for A0A1D0AST6 (Staphylococcus aureus) Explore A0A1D0AST6 Go to UniProtKB: A0A1D0AST6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1D0AST6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA 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]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PAR (Subject of Investigation/LOI) Query on PAR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PAROMOMYCIN C₂₃ H₄₅ N₅ O₁₄ UOZODPSAJZTQNH-LSWIJEOBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.249 (Depositor), 0.249 (DCC)
R-Value Work: 0.223 (Depositor), 0.223 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.748	α = 90
b = 133.748	β = 90
c = 133.748	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-02

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2022-11-02
Type: Initial release
Version 1.1: 2023-01-25
Changes: Structure summary
Version 1.2: 2023-10-25
Changes: Data collection, Refinement description
Version 1.3: 2023-11-29
Changes: Database references
Version 1.4: 2024-02-14
Changes: Database references
Version 1.5: 2026-02-25
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.