3III | pdb_00003iii

1.95 Angstrom Crystal Structure of CocE/NonD family hydrolase (SACOL2612) from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3III/pdb

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


• Deposited: 2009-08-01 Released: 2009-08-18 
• Deposition Author(s): Osinski, T., Chruszcz, M., Domagalski, M.J., Cymborowski, M., Shumilin, I.A., Skarina, T., Onopriyenko, O., Zimmerman, M.D., Savchenko, A., Edwards, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.183 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

1.95 Angstrom Crystal Structure of CocE/NonD family hydrolase (SACOL2612) from Staphylococcus aureus

Osinski, T., Chruszcz, M., Domagalski, M.J., Cymborowski, M., Shumilin, I.A., Skarina, T., Onopriyenko, O., Zimmerman, M.D., Savchenko, A., Edwards, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 65.39 kDa 
• Atom Count: 5,164 
• Modeled Residue Count: 556 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CocE/NonD family hydrolase	A	560	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: SACOL2612
UniProt
Find proteins for A0A0H2WZL3 (Staphylococcus aureus (strain COL)) Explore A0A0H2WZL3  Go to UniProtKB:  A0A0H2WZL3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	G [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.183 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33III

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.498	α = 90
b = 74.498	β = 90
c = 210.681	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
CCP4	model building
O	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Osinski, T., Chruszcz, M., Domagalski, M.J., Cymborowski, M., Shumilin, I.A., Skarina, T., Onopriyenko, O., Zimmerman, M.D., Savchenko, A., Edwards, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Structure summary