3HFR

Crystal structure of glutamate racemase from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb3HFR/pdb

• Classification: ISOMERASE
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-12 Released: 2009-06-09 
• Deposition Author(s): Majorek, K.A., Chruszcz, M., Zimmerman, M.D., Klimecka, M.M., Cymborowski, M., Skarina, T., Onopriyenko, O., Stam, J., Otwinowski, Z., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.244 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of glutamate racemase from Listeria monocytogenes

Majorek, K.A., Chruszcz, M., Zimmerman, M.D., Klimecka, M.M., Cymborowski, M., Skarina, T., Onopriyenko, O., Stam, J., Otwinowski, Z., Anderson, W.F., Savchenko, A., 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.

Macromolecule Content

• Total Structure Weight: 61.49 kDa 
• Atom Count: 4,381 
• Modelled Residue Count: 532 
• 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	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
JEF	E [auth A], F [auth A], H [auth B]	O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) C30 H63 N O10 ICCXIDTYQFYPNV-RUMGZKRTSA-N
CL	C [auth A], D [auth A], G [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: 2.30 Å
• R-Value Free:  0.244 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33HFR

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.651	α = 90
b = 66.651	β = 90
c = 257.99	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: 2009-06-09 
Deposition Author(s): Majorek, K.A., Chruszcz, M., Zimmerman, M.D., Klimecka, M.M., Cymborowski, M., Skarina, T., Onopriyenko, O., Stam, J., Otwinowski, Z., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2018-10-03
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 2.2: 2024-11-06
  Changes: Data collection, Structure summary