3B59

Crystal structure of the Mn(II)-bound glyoxalase from Novosphingobium aromaticivorans

• PDB DOI: https://doi.org/10.2210/pdb3B59/pdb

• Classification: LYASE
• Organism(s): Novosphingobium aromaticivorans DSM 12444
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-25 Released: 2007-11-06 
• Deposition Author(s): Madegowda, M., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.257 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal structure of the Mn(II)-bound glyoxalase from Novosphingobium aromaticivorans.

Madegowda, M., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 207.77 kDa 
• Atom Count: 14,236 
• Modelled Residue Count: 1,806 
• Deposited Residue Count: 1,860 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B, C, D, E, F	310	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0  Gene Names: Saro_0713
UniProt
Find proteins for Q2GAG3 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2GAG3  Go to UniProtKB:  Q2GAG3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.257 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.997	α = 90
b = 168.348	β = 90
c = 202.79	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Madegowda, M., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary