3V68 | pdb_00003v68

Crystal structure of Pyrococcus furiosus PF2050, a member of DUF2666 family protein

• PDB DOI: https://doi.org/10.2210/pdb3V68/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-19 Released: 2012-04-18 
• Deposition Author(s): Han, B.G., Lee, B.I.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of Pyrococcus furiosus PF2050, a member of the DUF2666 protein family

Han, B.G., Jeong, K.C., Cho, J.W., Jeong, B.C., Song, H.K., Lee, J.Y., Shin, D.H., Lee, S., Lee, B.I.

(2012) FEBS Lett 586: 1384-1388

• PubMed: 22616997 
• DOI: https://doi.org/10.1016/j.febslet.2012.04.004
• Primary Citation Related Structures: 
  3V68


• PubMed Abstract: 
  

  Pyrococcus furiosus PF2050 is an uncharacterized putative protein that contains two DUF2666 domains. Functional and structural studies of PF2050 have not previously been performed. In this study, we determined the crystal structure of PF2050. The structure of PF2050 showed that the two DUF2666 domains interact tightly, forming a globular structure. Each DUF2666 domain comprises an antiparallel β-sheet and an α-helical bundle. One side of the PF2050 structure has a positively charged basic cleft, which may have a DNA-binding function. Furthermore, we confirmed that PF2050 interacts with circular and linear dsDNA.

---

Organizational Affiliation: 
• Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 29.06 kDa 
• Atom Count: 2,287 
• Modeled Residue Count: 248 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	252	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF2050
UniProt
Find proteins for Q8TZE5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZE5  Go to UniProtKB:  Q8TZE5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.722	α = 90
b = 66.531	β = 96.56
c = 46.372	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Han, B.G., Lee, B.I.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations