3GC2 | pdb_00003gc2

1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase from Salmonella typhimurium in Complex with Succinic Acid

• PDB DOI: https://doi.org/10.2210/pdb3GC2/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-21 Released: 2009-03-10 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.185 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase from Salmonella typhimurium in Complex with Succinic Acid

Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., 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: 36.54 kDa 
• Atom Count: 3,044 
• Modeled Residue Count: 322 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
o-succinylbenzoate synthase	A	323	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: menC, STM2306 EC: 4.2.1.113
UniProt
Find proteins for P58486 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P58486  Go to UniProtKB:  P58486

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SIN	B [auth A], C [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
CL	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 1.85 Å
• R-Value Free:  0.185 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33gc2

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.968	α = 90
b = 149.968	β = 90
c = 39.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary