3DDM | pdb_00003ddm

CRYSTAL STRUCTURE OF MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME FROM Bordetella bronchiseptica RB50

• PDB DOI: https://doi.org/10.2210/pdb3DDM/pdb

• Classification: LYASE
• Organism(s): Bordetella bronchiseptica
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-06-05 Released: 2008-06-24 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Gerlt, J.A., 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: 2.60 Å
• R-Value Free: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

CRYSTAL STRUCTURE OF MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME FROM Bordetella bronchiseptica RB50

Fedorov, A.A., Fedorov, E.A., Toro, R., Sauder, M.J., Burley, S.K., Gerlt, J.A., Almo, S.C.

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 and 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 164.71 kDa 
• Atom Count: 10,762 
• Modeled Residue Count: 1,452 
• Deposited Residue Count: 1,568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative mandelate racemase/muconate lactonizing enzyme	A, B, C, D	392	Bordetella bronchiseptica	Mutation(s): 1  Gene Names: BB2459
UniProt
Find proteins for A0A0H3LM82 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LM82  Go to UniProtKB:  A0A0H3LM82

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.6	α = 90
b = 122.636	β = 90
c = 164.544	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Gerlt, J.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.3: 2021-10-20
  Changes: Database references
• Version 1.4: 2024-02-21
  Changes: Data collection