3OO2 | pdb_00003oo2

2.37 Angstrom resolution crystal structure of an alanine racemase (alr) from Staphylococcus aureus subsp. aureus COL

• PDB DOI: https://doi.org/10.2210/pdb3OO2/pdb

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-30 Released: 2010-10-06 
• Deposition Author(s): Halavaty, A.S., Shuvalova, L., Minasov, G., Winsor, J., Dubrovska, I., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

2.37 Angstrom resolution crystal structure of an alanine racemase (alr) from Staphylococcus aureus subsp. aureus COL

Halavaty, A.S., Shuvalova, L., Minasov, G., Winsor, J., Dubrovska, I., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.77 kDa 
• Atom Count: 6,061 
• Modeled Residue Count: 743 
• Deposited Residue Count: 770 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase 1	A, B	385	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: alr, alr1, SACOL2060 EC: 5.1.1.1
UniProt
Find proteins for Q5HED1 (Staphylococcus aureus (strain COL)) Explore Q5HED1  Go to UniProtKB:  Q5HED1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
BME	D [auth A], E [auth A], H [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
NA	C [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33oo2

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.735	α = 90
b = 118.31	β = 90
c = 129.008	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Halavaty, A.S., Shuvalova, L., Minasov, G., Winsor, J., Dubrovska, I., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description