6MN1

Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, mutant H168A in abortive complex with gentamicin-CoA

• PDB DOI: https://doi.org/10.2210/pdb6MN1/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-10-01 Released: 2018-10-24 
• Deposition Author(s): Stogios, P.J., Skarina, T., Michalska, K., Xu, Z., Yim, V., Savchenko, A., Joachimiak, A., Satchell, K.J., 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: 2.25 Å
• R-Value Free: 0.210 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, mutant H168A in abortive complex with gentamicin-CoA

Stogios, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 62.11 kDa 
• Atom Count: 4,828 
• Modelled Residue Count: 519 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside N(3)-acetyltransferase	A, B	263	uncultured bacterium	Mutation(s): 1  EC: 2.3.1.81
UniProt
Find proteins for A0A059X981 (uncultured bacterium) Explore A0A059X981  Go to UniProtKB:  A0A059X981

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	C [auth A], N [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
PE3	H [auth A], I [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
LLL	D [auth A], O [auth B]	(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL C19 H39 N5 O7 VEGXETMJINRLTH-BOZYPMBZSA-N
SO4	F [auth A], G [auth A], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A], K [auth A], L [auth A], M [auth A], S [auth B], T [auth B], U [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.210 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.337	α = 90
b = 127.337	β = 90
c = 95.271	γ = 120

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

Currently 6MN1 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Stogios, P.J., Skarina, T., Michalska, K., Xu, Z., Yim, V., Savchenko, A., Joachimiak, A., Satchell, K.J., 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	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary