2PEB

Crystal structure of a putative dioxygenase (npun_f1925) from nostoc punctiforme pcc 73102 at 1.46 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PEB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nostoc punctiforme PCC 73102
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-02 Released: 2007-04-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.213 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Crystal structure of putative dioxygenase (ZP_00109509.1) from Nostoc punctiforme PCC 73102 at 1.46 A resolution

Joint Center for Structural Genomics (JCSG)

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.

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 28.14 kDa 
• Atom Count: 2,141 
• Modelled Residue Count: 230 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative dioxygenase	A, B	122	Nostoc punctiforme PCC 73102	Mutation(s): 0  Gene Names: ZP_00109509.1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ZN	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	D [auth A], H [auth B]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.213 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M32PEB

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.562	α = 90
b = 57.042	β = 104.81
c = 46.676	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-04-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence