4N57 | pdb_00004n57

Crystal structure of aminoglycoside phosphotransferase APH(2'')-IVa ADP complex

• PDB DOI: https://doi.org/10.2210/pdb4N57/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus casseliflavus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-10-09 Released: 2014-12-17 
• Deposition Author(s): Kaplan, E., Leban, N., Chaloin, L., Guichou, J.-F., Lionne, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.248 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of aminoglycoside phosphotransferase APH(2'')-IVa ADP complex

Kaplan, E., Leban, N., Chaloin, L., Guichou, J.-F., Lionne, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.14 kDa 
• Atom Count: 5,240 
• Modeled Residue Count: 593 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APH(2'')-Id	A, B	321	Enterococcus casseliflavus	Mutation(s): 2  Gene Names: aph(2'')-Id
UniProt
Find proteins for O68183 (Enterococcus casseliflavus) Explore O68183  Go to UniProtKB:  O68183

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth A], D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.248 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.051	α = 90
b = 65.802	β = 92.43
c = 76.731	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
DNA	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Kaplan, E., Leban, N., Chaloin, L., Guichou, J.-F., Lionne, C.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Advisory, Data collection, Refinement description
• Version 1.2: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description