2OO6 | pdb_00002oo6

Crystal structure of putative L-alanine-DL-glutamate epimerase from Burkholderia xenovorans strain LB400

• PDB DOI: https://doi.org/10.2210/pdb2OO6/pdb

• Classification: ISOMERASE
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-25 Released: 2007-02-06 
• Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Wu, B., Sridhar, V., Freeman, J., Smyth, L., Atwell, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.192 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal structure of putative L-alanine-DL-glutamate epimerase from Burkholderia xenovorans strain LB400

Bonanno, J.B., Dickey, M., Bain, K.T., Wu, B., Sridhar, V., Freeman, J., Smyth, L., Atwell, S., 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: 46.15 kDa 
• Atom Count: 3,500 
• Modeled Residue Count: 393 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.192 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.906	α = 90
b = 104.906	β = 90
c = 145.658	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Wu, B., Sridhar, V., Freeman, J., Smyth, L., Atwell, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2012-10-24
  Changes: Structure summary
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-12-27
  Changes: Data collection, Database references