2QDR | pdb_00002qdr

Crystal structure of a putative dioxygenase (npun_f5605) from nostoc punctiforme pcc 73102 at 2.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2QDR/pdb

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


• Deposited: 2007-06-21 Released: 2007-07-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Crystal structure of uncharacterized protein (ZP_00345151.1) from Nostoc punctiforme PCC 73102 at 2.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.49 kDa 
• Atom Count: 4,599 
• Modeled Residue Count: 569 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	303	Nostoc punctiforme PCC 73102	Mutation(s): 0  Gene Names: ZP_00345151.1
UniProt
Find proteins for B2J7U5 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J7U5  Go to UniProtKB:  B2J7U5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A], E [auth A], G [auth B], H [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
UNL	C [auth A], F [auth B]	Unknown ligand JKMHFZQWWAIEOD-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: 2.60 Å
• R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32QDR

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.096	α = 90
b = 102.096	β = 90
c = 250.807	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-07-24
  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
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary