5CLF | pdb_00005clf

Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) from the acidophilic bacterium Acetobacter aceti, at pH 8.5

• PDB DOI: https://doi.org/10.2210/pdb5CLF/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: 2.00 Å
• R-Value Free: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2fw1

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: 38.17 kDa 
• Atom Count: 2,785 
• Modeled Residue Count: 323 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.43	α = 90
b = 99.43	β = 90
c = 164.168	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	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: 2017-11-08
  Changes: Source and taxonomy
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description