5ZC7 | pdb_00005zc7

Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (P63 space group).

• PDB DOI: https://doi.org/10.2210/pdb5ZC7/pdb

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


• Deposited: 2018-02-15 Released: 2019-02-20 
• Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis

Pavithra, G.C., Ramagopal, U.A.

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: 40.87 kDa 
• Atom Count: 2,943 
• Modeled Residue Count: 363 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE (Subject of Investigation/LOI)	D [auth A], I [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
ACT	H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI (Subject of Investigation/LOI)	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	F [auth A], G [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.074	α = 90
b = 121.074	β = 90
c = 50.035	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description