4S2U | pdb_00004s2u

Crystal structure of the Phosphorybosylpyrophosphate synthetase from E. Coli

• PDB DOI: https://doi.org/10.2210/pdb4S2U/pdb

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


• Deposited: 2015-01-23 Released: 2016-01-27 
• Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Muravieva, T.I., Iaroslavtceva, A.K., Stepanenko, V.N., Zhukhlistova, N.E., Esipov, R.S., Kuranova, I.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.304 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Crystal structure of the Phosphorybosylpyrophosphate synthetase from E. Coli

Timofeev, V.I., Abramchik, Y.A., Muravieva, T.I., Iaroslavtceva, A.K., Stepanenko, V.N., Zhukhlistova, N.E., Esipov, R.S., Kuranova, I.P.

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)

Macromolecule Content 

• Total Structure Weight: 34.35 kDa 
• Atom Count: 2,351 
• Modeled Residue Count: 308 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-phosphate pyrophosphokinase	A	316	Escherichia coli	Mutation(s): 0  Gene Names: prsA, prs EC: 2.7.6.1
UniProt
Find proteins for P0A717 (Escherichia coli (strain K12)) Explore P0A717  Go to UniProtKB:  P0A717

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.304 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.599	α = 90
b = 104.599	β = 90
c = 125.78	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Muravieva, T.I., Iaroslavtceva, A.K., Stepanenko, V.N., Zhukhlistova, N.E., Esipov, R.S., Kuranova, I.P.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Experimental preparation