3KOL | pdb_00003kol

Crystal structure of a glyoxalase/dioxygenase from Nostoc punctiforme

• PDB DOI: https://doi.org/10.2210/pdb3KOL/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Nostoc punctiforme PCC 73102
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-11-13 Released: 2009-11-24 
• Deposition Author(s): Eswaramoorthy, S., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal structure of a glyoxalase/dioxygenase from Nostoc punctiforme

Eswaramoorthy, S., Burley, S.K., 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: 17.28 kDa 
• Atom Count: 1,238 
• Modeled Residue Count: 146 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A	156	Nostoc punctiforme PCC 73102	Mutation(s): 0  Gene Names: Npun_R6391
UniProt
Find proteins for B2IY64 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2IY64  Go to UniProtKB:  B2IY64

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-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:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.382	α = 90
b = 50.382	β = 90
c = 138.026	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Eswaramoorthy, S., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary