6NMN | pdb_00006nmn

Ternary complex structure of the T130K mutant of ANT-4'' with Neomycin and ATP (No Pyrophosphate)

• PDB DOI: https://doi.org/10.2210/pdb6NMN/pdb

• Classification: transferase/ANTIBIOTIC
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2019-01-11 Released: 2020-01-15 
• Deposition Author(s): Cuneo, M.J., Selvaraj, B.
• Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Catch and release: A novel variation of the archetypal nucleotidyl transfer reaction

Selvaraj, B., Cuneo, M.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: 60.27 kDa 
• Atom Count: 4,838 
• Modeled Residue Count: 506 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kanamycin nucleotidyltransferase	A, B	256	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.7.7
UniProt
Find proteins for P05057 (Staphylococcus aureus) Explore P05057  Go to UniProtKB:  P05057

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMY	C [auth A], H [auth B]	NEOMYCIN C23 H46 N6 O13 PGBHMTALBVVCIT-VCIWKGPPSA-N
AMP	D [auth A], I [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.05	α = 90
b = 58.05	β = 90
c = 363.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Cuneo, M.J., Selvaraj, B.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 2.0: 2024-05-29
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary