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


This is version 2.2 of the entry. See complete history. 


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 10: 1219-1229

  • DOI: https://doi.org/10.1002/2211-5463.12837
  • Primary Citation of Related Structures:  
    6LKP

  • 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 nonheterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic nonheterocystous 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: 

    Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA protection during starvation protein
A, B, C, D, E
A, B, C, D, E, F
184Leptolyngbya sp. O-77Mutation(s): 0 
EC: 1.16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
BA [auth F]
G [auth A]
H [auth A]
K [auth A]
L [auth B]
BA [auth F],
G [auth A],
H [auth A],
K [auth A],
L [auth B],
O [auth B],
P [auth B],
S [auth C],
T [auth D],
U [auth D],
X [auth D],
Y [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE
Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
DA [auth F]
I [auth A]
J [auth A]
AA [auth E],
CA [auth F],
DA [auth F],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
V [auth D],
W [auth D],
Z [auth E]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
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

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 2.0: 2020-04-01
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2020-09-30
    Changes: Database references, Derived calculations
  • Version 2.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description