7W1A

Crystal Structure of MPH-E in complex with GMP and Azithromycin

• PDB DOI: https://doi.org/10.2210/pdb7W1A/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-11-19 Released: 2023-04-26 
• Deposition Author(s): Qi, Q., Kuang, L., Jiang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Acinetobacter baumannii Macrolide Phosphotransferases E Reveal the Novel Catalysis Mechanism

Qi, Q., Kuang, L., Jiang, Y.

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 Evidence: gel filtration

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: 71.3 kDa 
• Atom Count: 4,836 
• Modelled Residue Count: 574 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide 2'-phosphotransferase	A [auth B], B [auth A]	302	Acinetobacter baumannii	Mutation(s): 0  Gene Names: mph(E)
UniProt
Find proteins for A5Y459 (Acinetobacter baumannii) Explore A5Y459  Go to UniProtKB:  A5Y459

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZIT (Subject of Investigation/LOI)	D [auth B], F [auth A]	AZITHROMYCIN C38 H72 N2 O12 MQTOSJVFKKJCRP-BICOPXKESA-N
GMP (Subject of Investigation/LOI)	C [auth B], E [auth A]	GUANOSINE C10 H13 N5 O5 NYHBQMYGNKIUIF-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.014	α = 90
b = 45.852	β = 105.71
c = 89.677	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Qi, Q., Kuang, L., Jiang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2019YJ0083

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description