6LKP

Crystal structure of Dps1 from the thermophilic non-heterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O-77


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.257 

wwPDB Validation 3D Report Full Report



Literature

Biochemical and structural characterization of a thermostable Dps protein with His-type ferroxidase centers and outer metal-binding sites.

Minato, T.Teramoto, T.Kakuta, Y.Ogo, S.Yoon, K.S.

(2020) FEBS Open Bio 

  • DOI: 10.1002/2211-5463.12837
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The DNA-binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from non-heterocystous filamentous cyanobacteria. In this study, a Dps protei ...

    The DNA-binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from non-heterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic non-heterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O-77 (TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 demonstrated that it had higher thermostability than previously reported Dps proteins. X-ray crystallographic analysis revealed that TlDps1 possessed His-type ferroxidase centers within the cavity and unique metal binding sites located on the surface of the protein, which presumably contributed to its exceedingly high thermostability.


    Organizational Affiliation

    Center for Small Molecule Energy, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA protection during starvation protein
A, B, C, D, E, F
184Leptolyngbya sp. O-77Mutation(s): 0 
Gene Names: dps_2O77CONTIG1_04170
EC: 1.16
Find proteins for A0A0X8WZ56 (Leptolyngbya sp. O-77)
Go to UniProtKB:  A0A0X8WZ56
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, B, C, D, E, F
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.257 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.787α = 90
b = 92.787β = 90
c = 261.12γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJPMJCR18R2

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 2.0: 2020-04-01
    Changes: Atomic model, Data collection, Derived calculations