7JM2 | pdb_00007jm2

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with apramycin

• PDB DOI: https://doi.org/10.2210/pdb7JM2/pdb

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


• Deposited: 2020-07-30 Released: 2020-09-16 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Bordeleau, E., Wright, G.D., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with apramycin

Stogios, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.11 kDa 
• Atom Count: 7,455 
• Modeled Residue Count: 817 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminocyclitol acetyltransferase ApmA	A, B, C	274	Staphylococcus aureus	Mutation(s): 0  Gene Names: apmA
UniProt
Find proteins for A0A1D0AST6 (Staphylococcus aureus) Explore A0A1D0AST6  Go to UniProtKB:  A0A1D0AST6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AM2 (Subject of Investigation/LOI)	D [auth A], E [auth B], G [auth C]	APRAMYCIN C21 H41 N5 O11 XZNUGFQTQHRASN-XQENGBIVSA-N
CL	F [auth B], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.73	α = 90
b = 107.536	β = 90
c = 138.696	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

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Bordeleau, E., Wright, G.D., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description