4MYM

Crystal structure of a glyoxalase/ bleomycin resistance protein/ dioxygenase from Nocardioides

• PDB DOI: https://doi.org/10.2210/pdb4MYM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nocardioides sp. JS614
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-27 Released: 2013-12-25 
• Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, F., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., AL Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.217 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Crystal structure of a glyoxalase/ bleomycin resistance protein/ dioxygenase from Nocardioides.

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

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)

Macromolecule Content

• Total Structure Weight: 19.98 kDa 
• Atom Count: 1,249 
• Modelled Residue Count: 151 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A	176	Nocardioides sp. JS614	Mutation(s): 0  Gene Names: Noca_4190
UniProt
Find proteins for A1SPF2 (Nocardioides sp. (strain ATCC BAA-499 / JS614)) Explore A1SPF2  Go to UniProtKB:  A1SPF2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	B [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-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: 1.90 Å
• R-Value Free: 0.217 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.66	α = 90
b = 83.589	β = 90
c = 102.413	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, F., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., AL Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary