6P06 | pdb_00006p06

Ternary structure of the E52D mutant of ANT-4 with Neomycin and AMPCPP

• PDB DOI: https://doi.org/10.2210/pdb6P06/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Bacillus sp. (in: firmicutes)
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): Yes 


• Deposited: 2019-05-16 Released: 2020-01-29 
• Deposition Author(s): Selvaraj, B., Cuneo, M.J.
• 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: 2.30 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (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 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.64 kDa 
• Atom Count: 4,447 
• 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	Bacillus sp. (in: firmicutes)	Mutation(s): 1  Gene Names: knt, kan 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 (Subject of Investigation/LOI)	C [auth A], G [auth A]	NEOMYCIN C23 H46 N6 O13 PGBHMTALBVVCIT-VCIWKGPPSA-N
APC (Subject of Investigation/LOI)	D [auth A], I [auth B]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C11 H18 N5 O12 P3 CAWZRIXWFRFUQB-IOSLPCCCSA-N
CA (Subject of Investigation/LOI)	E [auth A], F [auth A], H [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.71	α = 90
b = 97.95	β = 90
c = 100.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Selvaraj, B., Cuneo, M.J.

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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: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references
• Version 1.2: 2020-05-20
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations