6UN8 | pdb_00006un8

Wild type ANT bound to neomycin

• PDB DOI: https://doi.org/10.2210/pdb6UN8/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-10-11 Released: 2020-05-06 
• Deposition Author(s): Cuneo, M.J., Selvaraj, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.198 (Depositor) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

"Catch and Release": a Variation of the Archetypal NucleotidylTransfer Reaction

Selvaraj, B., Kocaman, S., Trifas, M., Serpersu, E.H., Cuneo, M.J.

(2020) ACS Catal 10: 3548-3555

• DOI: https://doi.org/10.1021/acscatal.9b05201

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)

Macromolecule Content 

• Total Structure Weight: 58.9 kDa 
• Atom Count: 4,739 
• Modeled Residue Count: 505 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside NucleotidylTransferase	A, B	253	Staphylococcus aureus	Mutation(s): 0  Gene Names: knt, kan EC: 2.7.7
UniProt
Find proteins for P05057 (Staphylococcus aureus) Explore P05057  Go to UniProtKB:  P05057

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMY (Subject of Investigation/LOI)	C [auth A], E [auth B]	NEOMYCIN C23 H46 N6 O13 PGBHMTALBVVCIT-VCIWKGPPSA-N
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.198 (Depositor) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.661	α = 90
b = 97.794	β = 90
c = 102.231	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Currently 6UN8 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Cuneo, M.J., Selvaraj, B.

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description