6NMK | pdb_00006nmk

Binary complex structure of the T130K mutant of ANT-4'' with Neomycin

• PDB DOI: https://doi.org/10.2210/pdb6NMK/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: 1.94 Å
• R-Value Free: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

'Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction

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

(2020) ACS Catal 

• 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.59 kDa 
• Atom Count: 4,678 
• Modeled Residue Count: 505 
• 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], G [auth B]	NEOMYCIN C23 H46 N6 O13 PGBHMTALBVVCIT-VCIWKGPPSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59	α = 90
b = 97.71	β = 90
c = 101.97	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: 2020-05-06
  Changes: Database references
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations