3SN1 | pdb_00003sn1

Crystal structure of putative L-alanine-DL-glutamate epimerase from Burkholderia xenovorans strain LB400 bound to magnesium and tartrate

• PDB DOI: https://doi.org/10.2210/pdb3SN1/pdb

• Classification: Structural Genomics, unknown function
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-28 Released: 2011-07-27 
• Deposition Author(s): Bonanno, J.B., Patskovsky, Y., Toro, R., Dickey, M., Bain, K.T., Wu, B., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.165 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of putative L-alanine-DL-glutamate epimerase from Burkholderia xenovorans strain LB400 bound to magnesium and tartrate

Bonanno, J.B., Patskovsky, Y., Toro, R., Dickey, M., Bain, K.T., Wu, B., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 46.51 kDa 
• Atom Count: 3,495 
• Modeled Residue Count: 396 
• Deposited Residue Count: 409 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative L-alanine-DL-glutamate epimerase	A	409	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: Bxeno_B1104, Bxe_B1897
UniProt
Find proteins for Q13PB7 (Paraburkholderia xenovorans (strain LB400)) Explore Q13PB7  Go to UniProtKB:  Q13PB7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAR	C [auth A]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.80 Å
• R-Value Free:  0.165 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.932	α = 90
b = 104.932	β = 90
c = 145.145	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Bonanno, J.B., Patskovsky, Y., Toro, R., Dickey, M., Bain, K.T., Wu, B., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary