9IYG

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the 17-mer expression tag bound in the substrate binding site of a neighbouring molecule at 2.60 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb9IYG/pdb

• Classification: TRANSFERASE
• Organism(s): Enterobacter sp. 638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-30 Released: 2024-08-21 
• Deposition Author(s): Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.
• Funding Organization(s): Indian Council of Medical Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 

Starting Model: experimental

Literature

Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the 17-mer expression tag bound in the substrate binding site of a neighbouring molecule at 2.60 A resolution.

Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.

To be published.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.03 kDa 
• Atom Count: 8,271 
• Modelled Residue Count: 988 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A, B, C, D, E, F	176	Enterobacter sp. 638	Mutation(s): 0  Gene Names: coaD, Ent638_0105 EC: 2.7.7.3
UniProt
Find proteins for A4W515 (Enterobacter sp. (strain 638)) Explore A4W515  Go to UniProtKB:  A4W515

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	G [auth A], H [auth B], I [auth C], J [auth D], L [auth E], M [auth F]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.271	α = 90
b = 79.846	β = 93.354
c = 107.541	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
autoPROC	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	I-1251

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release