8OKH

Crystal structure of Bdellovibrio bacteriovorus Bd1399


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Protein target highlights in CASP15: Analysis of models by structure providers.

Alexander, L.T.Durairaj, J.Kryshtafovych, A.Abriata, L.A.Bayo, Y.Bhabha, G.Breyton, C.Caulton, S.G.Chen, J.Degroux, S.Ekiert, D.C.Erlandsen, B.S.Freddolino, P.L.Gilzer, D.Greening, C.Grimes, J.M.Grinter, R.Gurusaran, M.Hartmann, M.D.Hitchman, C.J.Keown, J.R.Kropp, A.Kursula, P.Lovering, A.L.Lemaitre, B.Lia, A.Liu, S.Logotheti, M.Lu, S.Markusson, S.Miller, M.D.Minasov, G.Niemann, H.H.Opazo, F.Phillips Jr., G.N.Davies, O.R.Rommelaere, S.Rosas-Lemus, M.Roversi, P.Satchell, K.Smith, N.Wilson, M.A.Wu, K.L.Xia, X.Xiao, H.Zhang, W.Zhou, Z.H.Fidelis, K.Topf, M.Moult, J.Schwede, T.

(2023) Proteins 91: 1571-1599

  • DOI: https://doi.org/10.1002/prot.26545
  • Primary Citation of Related Structures:  
    8OKH, 8SMQ

  • PubMed Abstract: 

    We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.


  • Organizational Affiliation

    Biozentrum, University of Basel, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF2807 domain-containing protein
A, B
175Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: Bd1399
UniProt
Find proteins for Q6MN62 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MN62 
Go to UniProtKB:  Q6MN62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MN62
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.159α = 90
b = 90.159β = 90
c = 112.552γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom209437/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references