3GRI | pdb_00003gri

The Crystal Structure of a Dihydroorotase from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3GRI/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus MW2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-25 Released: 2009-05-19 
• Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Skarina, T., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

The Crystal Structure of a Dihydroorotase from Staphylococcus aureus

Brunzelle, J.S., Wawrzak, Z., Skarina, T., Onopriyenko, O., Savchenko, A., Anderson, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.1 kDa 
• Atom Count: 6,952 
• Modeled Residue Count: 845 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotase	A, B	424	Staphylococcus aureus subsp. aureus MW2	Mutation(s): 0  Gene Names: MW1084, pyrC, pyrC SACOL1213 EC: 3.5.2.3
UniProt
Find proteins for P65907 (Staphylococcus aureus (strain MW2)) Explore P65907  Go to UniProtKB:  P65907

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A], G [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [auth A], E [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33gri

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.217	α = 88.33
b = 55.229	β = 76.56
c = 85.647	γ = 76.97

Software Package:

Software Name	Purpose
BLU-MAX	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Skarina, T., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2024-11-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary