5B6H | pdb_00005b6h

Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP.

• PDB DOI: https://doi.org/10.2210/pdb5B6H/pdb

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


• Deposited: 2016-05-27 Released: 2017-05-31 
• Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP.

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: 20.02 kDa 
• Atom Count: 1,442 
• Modeled Residue Count: 179 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase	A	181	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
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.875	α = 90
b = 78.554	β = 116.56
c = 53.885	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description