8XRW | pdb_00008xrw

crystal structure of HpPPAT in complex with ATP

• PDB DOI: https://doi.org/10.2210/pdb8XRW/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-08 Released: 2024-10-30 
• Deposition Author(s): Yin, H.S.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

crystal structure of HpPPAT in complex with ATP

Yin, H.S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 213.82 kDa 
• Atom Count: 15,196 
• Modeled Residue Count: 1,874 
• Deposited Residue Count: 1,884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A [auth I], B [auth J], C [auth L], D [auth A], E [auth B], F [auth C], G [auth D], H [auth E], I [auth F], J [auth G], K [auth H], L [auth K]	157	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: coaD, kdtB, HP_1475 EC: 2.7.7.3
UniProt
Find proteins for O26010 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O26010  Go to UniProtKB:  O26010

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	M [auth I], N [auth J], O [auth L]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.15	α = 88.02
b = 82.06	β = 73.55
c = 105.512	γ = 87.14

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Yin, H.S.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release