8ZXR | pdb_00008zxr

Crystal structure of Ssr1698 in complex with heme c

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: in silico
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Literature

Structural Basis for Monomer-Dimer Transition of Dri1 Upon Heme Binding.

Wang, X.Y., Zhang, J., Li, H.Y., Dong, C.S., Dai, H.E., Wang, M., Liu, L.

(2025) Proteins 93: 949-956

  • DOI: https://doi.org/10.1002/prot.26778
  • Primary Citation of Related Structures:  
    8ZXQ, 8ZXR

  • PubMed Abstract: 

    Domain related to iron (DRI) contains approximately 90 residues and is involved in iron and heme metabolism. Recent discoveries have annotated Dri1, a DRI-only protein from the cyanobacterium Synechocystis, as a regulator of succinate dehydrogenase in a b-type heme-dependent manner or as a c-type heme oxygenase. Here, we report high-resolution structures of Dri1 in complex with b-type and c-type hemes, respectively. Bis-His-ligated heme is located in the middle of the dimeric Dri1 complex with heme b, as well as in the complex of monomeric Dri1 with c-type heme, but distinct heme binding modes are revealed. Structural analyses suggest that Dri1 may participate in the succinate dehydrogenase activity and/or the metabolism of cytochromes.

    • Organizational Affiliation: 
    • School of Life Sciences, Anhui University, Hefei, Anhui, China.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ssr1698 protein105Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: ssr1698
UniProt
Find proteins for P73129 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P73129 
Go to UniProtKB:  P73129
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP73129
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c11Equus caballusMutation(s): 0 
UniProt
Find proteins for P00004 (Equus caballus)
Explore P00004 
Go to UniProtKB:  P00004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00004
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.597α = 90
b = 83.597β = 90
c = 69.3γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references