4MB6

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis.

• PDB DOI: https://doi.org/10.2210/pdb4MB6/pdb

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


• Deposited: 2013-08-19 Released: 2013-09-04 
• Deposition Author(s): Pavithra, G.C., Kim, J., Hegde, R.P., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.238 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis

Pavithra, G.C., Kim, J., Hegde, R.P., Almo, S.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: 20.19 kDa 
• Atom Count: 1,429 
• Modelled Residue Count: 183 
• Deposited Residue Count: 187 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.238 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.56	α = 90
b = 78.38	β = 112.98
c = 54.01	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Pavithra, G.C., Kim, J., Hegde, R.P., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description