3OUT

Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate.

• PDB DOI: https://doi.org/10.2210/pdb3OUT/pdb

• Classification: ISOMERASE
• Organism(s): Francisella tularensis subsp. tularensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-15 Released: 2010-09-29 
• Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Kudriska, M., Edwards, A., Savchenko, A., Anderson, F.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: 0.193 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate.

Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Kudriska, M., Edwards, A., Savchenko, A., Anderson, F.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 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.26 kDa 
• Atom Count: 6,958 
• Modelled Residue Count: 791 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate racemase	A, B, C	268	Francisella tularensis subsp. tularensis	Mutation(s): 0  Gene Names: FTT_1197c, murI EC: 5.1.1.3
UniProt
Find proteins for Q5NFN6 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NFN6  Go to UniProtKB:  Q5NFN6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGL	D [auth A], E [auth B], F [auth C]	D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	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: 0.193 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/m33out

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.06	α = 90
b = 98.06	β = 90
c = 154.15	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CCP4	model building
MrBUMP	phasing
PHENIX	model building
REFMAC	refinement
XSCALE	data scaling
CCP4	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Kudriska, M., Edwards, A., Savchenko, A., Anderson, F.W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-09-29
  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: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary