3IST | pdb_00003ist

Crystal structure of glutamate racemase from Listeria monocytogenes in complex with succinic acid

• PDB DOI: https://doi.org/10.2210/pdb3IST/pdb

• Classification: ISOMERASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-27 Released: 2009-09-22 
• Deposition Author(s): Majorek, K.A., Chruszcz, M., Skarina, T., Onopriyenko, O., Stam, J., Anderson, W.F., Savchenko, A., Bujnicki, J.M., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.211 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glutamate racemase from Listeria monocytogenes in complex with succinic acid

Majorek, K.A., Chruszcz, M., Skarina, T., Onopriyenko, O., Stam, J., Anderson, W.F., Savchenko, A., Bujnicki, J.M., Minor, W., 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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.9 kDa 
• Atom Count: 4,704 
• Modeled Residue Count: 534 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate racemase	A, B	269	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo1237, murI, racE EC: 5.1.1.3
UniProt
Find proteins for Q8Y7N7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y7N7  Go to UniProtKB:  Q8Y7N7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	C [auth A], E [auth B]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
CL	D [auth A], F [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: 1.65 Å
• R-Value Free:  0.211 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33IST

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.42	α = 90
b = 66.42	β = 90
c = 258.774	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-3000	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Majorek, K.A., Chruszcz, M., Skarina, T., Onopriyenko, O., Stam, J., Anderson, W.F., Savchenko, A., Bujnicki, J.M., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-09-22
  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: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary