5CLI | pdb_00005cli

Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) from the acidophilic bacterium Acetobacter aceti, complexed with AIR (5-aminoimidazole ribonucleotide)

• PDB DOI: https://doi.org/10.2210/pdb5CLI/pdb

• Classification: ISOMERASE
• Organism(s): Acetobacter aceti 1023
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-16 Released: 2016-07-27 
• Deposition Author(s): Starks, C.M., Kappock, T.J.
• Funding Organization(s): Herman Frasch Foundation, National Science Foundation (NSF, United States), Department of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.173 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Structure of a single tryptophan mutant of Acetobacter aceti PurE

Sullivan, K.L., Tranchimand, S., Kappock, T.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.06 kDa 
• Atom Count: 2,843 
• Modeled Residue Count: 320 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N5-carboxyaminoimidazole ribonucleotide mutase	A, B	183	Acetobacter aceti 1023	Mutation(s): 0  Gene Names: purE, AZ09_02690 EC: 5.4.99.18

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AIR	C [auth A]	5-AMINOIMIDAZOLE RIBONUCLEOTIDE C8 H14 N3 O7 P PDACUKOKVHBVHJ-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.173 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.199	α = 90
b = 99.199	β = 90
c = 164.389	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Starks, C.M., Kappock, T.J.

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Funding Organization	Location	Grant Number
Herman Frasch Foundation	United States	531-HF02
National Science Foundation (NSF, United States)	United States	MCB0347250
Department of Education	United States	200A010213

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description