4Z7J | pdb_00004z7j

Structure of Acetobacter aceti PurE-S57A

• PDB DOI: https://doi.org/10.2210/pdb4Z7J/pdb

• Classification: ISOMERASE
• Organism(s): Acetobacter aceti 1023
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-04-07 Released: 2016-04-13 
• Deposition Author(s): Kappock, T.J., Sullivan, K.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Mutation of the conserved serine in two PurE classes

Sullivan, K.L., 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: 38.61 kDa 
• Atom Count: 2,896 
• Modeled Residue Count: 319 
• 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): 1  Gene Names: purE, AZ09_02690 EC: 5.4.99.18

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RP5	G [auth A]	5-O-phosphono-beta-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-TXICZTDVSA-N
PG0	K [auth B]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
SO4	L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT	D [auth A], I [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
ACT	C [auth A], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.362	α = 90
b = 99.362	β = 90
c = 165.353	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Kappock, T.J., Sullivan, K.L.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary