4YCB | pdb_00004ycb

Structure of a single tryptophan mutant of Acetobacter aceti PurE

• PDB DOI: https://doi.org/10.2210/pdb4YCB/pdb

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


• Deposited: 2015-02-19 Released: 2016-02-24 
• Deposition Author(s): Kappock, T.J., Sullivan, K.L., Mullins, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.141 (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: 38.4 kDa 
• Atom Count: 2,959 
• Modeled Residue Count: 322 
• 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): 2  Gene Names: purE, AZ09_02690 EC: 5.4.99.18

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGF	K [auth B]	2,5,8,11-TETRAOXATRIDECANE C9 H20 O4 JRRDISHSXWGFRF-UHFFFAOYSA-N
SO4	F [auth A], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
K	J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.803	α = 90
b = 99.803	β = 90
c = 164.409	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: 2016-02-24 
Deposition Author(s): Kappock, T.J., Sullivan, K.L., Mullins, E.A.

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Other
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description