2IGB | pdb_00002igb

Crystal Structure of PyrR, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, UMP-bound form

• PDB DOI: https://doi.org/10.2210/pdb2IGB/pdb

• Classification: TRANSFERASE
• Organism(s): [Bacillus] caldolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-22 Released: 2007-09-25 
• Deposition Author(s): Chander, P., Switzer, R.L., Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

PyrR, the regulator of the pyrimidine biosynthetic operon in Bacillus caldolyticus

Chander, P., Switzer, R.L., Smith, J.L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.95 kDa 
• Atom Count: 3,195 
• Modeled Residue Count: 345 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PyrR bifunctional protein	A, B	179	[Bacillus] caldolyticus	Mutation(s): 0  Gene Names: pyrR EC: 2.4.2.9
UniProt
Find proteins for P41007 (Bacillus caldolyticus) Explore P41007  Go to UniProtKB:  P41007

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	C [auth A], E [auth B]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
EDO	D [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.281	α = 90
b = 96.752	β = 90
c = 63.104	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Chander, P., Switzer, R.L., Smith, J.L.

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description