6IQC

Wild-type Programmed Cell Death 5 protein from Sulfolobus solfataricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the programmed cell death 5 protein from Sulfolobus solfataricus.

Lin, K.F.Hsu, J.Y.Hsieh, D.L.Tsai, M.J.Yeh, C.H.Chen, C.Y.

(2019) Acta Crystallogr F Struct Biol Commun 75: 73-79

  • DOI: https://doi.org/10.1107/S2053230X18017673
  • Primary Citation of Related Structures:  
    6IQC, 6IQO

  • PubMed Abstract: 

    Programmed cell death 5 (PDCD5) is a vital signaling protein in the apoptosis pathway in eukaryotes. It is known that there are two dissociated N-terminal regions and a triple-helix core in eukaryotic PDCD5. Structural and functional studies of PDCD5 from hyperthermophilic archaea have been limited to date. Here, the PDCD5 homolog Sso0352 (SsoPDCD5) was identified in Sulfolobus solfataricus, the SsoPDCD5 protein was expressed and crystallized, and the phase was identified by single-wavelength anomalous diffraction. The native SsoPDCD5 crystal belonged to space group C2 and diffracted to 1.49 Å resolution. This is the first crystal structure of a PDCD5 homolog to be solved. SsoPDCD5 shares a similar triple-helix bundle with eukaryotic PDCD5 but has a long α-helix in the N-terminus. A structural search and biochemical data suggest that SsoPDCD5 may function as a DNA-binding protein.


  • Organizational Affiliation

    Department of Life Sciences, National Central University, 300 Zhongda Road, Zhongli District, Taoyuan City 32001, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-binding protein SSO0352118Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: SSO0352
UniProt
Find proteins for Q980F8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q980F8 
Go to UniProtKB:  Q980F8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ980F8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.094α = 90
b = 36.634β = 98.4
c = 36.197γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description