6P08 | pdb_00006p08

Ternary structure of the E52D mutant of ANT-4'' with Neomycin, AMP and Pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb6P08/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: 2.27 Å
• R-Value Free: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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: 60.62 kDa 
• Atom Count: 4,438 
• Modeled Residue Count: 504 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kanamycin nucleotidyltransferase	A, B [auth D]	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMY (Subject of Investigation/LOI)	C [auth A], I [auth A]	NEOMYCIN C23 H46 N6 O13 PGBHMTALBVVCIT-VCIWKGPPSA-N
AMP (Subject of Investigation/LOI)	G [auth A], H [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
PPV (Subject of Investigation/LOI)	D [auth A], K [auth D]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth A], F [auth A], J [auth A], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.75	α = 90
b = 99.3	β = 90
c = 101.49	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: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description