5Y07 | pdb_00005y07

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis with PRPP.

• PDB DOI: https://doi.org/10.2210/pdb5Y07/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pseudotuberculosis IP 32953
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-25 Released: 2018-08-01 
• Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.235 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis with PRPP

Ramagopal, U.A., Pavithra, G.C.

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)

Macromolecule Content 

• Total Structure Weight: 41.21 kDa 
• Atom Count: 2,854 
• Modeled Residue Count: 357 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase	A, B	187	Yersinia pseudotuberculosis IP 32953	Mutation(s): 0  Gene Names: apt, YPTB0991 EC: 2.4.2.7
UniProt
Find proteins for Q66DQ2 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q66DQ2  Go to UniProtKB:  Q66DQ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRP	C [auth A], F [auth B]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	D [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.235 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.301	α = 90
b = 86.292	β = 105.87
c = 48.553	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary