8OKH | pdb_00008okh

Crystal structure of Bdellovibrio bacteriovorus Bd1399

PDB DOI: https://doi.org/10.2210/pdb8OKH/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Bdellovibrio bacteriovorus HD100
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-28 Released: 2023-10-25
Deposition Author(s): Caulton, S.G., Lovering, A.L.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.244 (Depositor), 0.241 (DCC)
R-Value Work:
0.186 (Depositor), 0.189 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 37493353 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.26545
Primary Citation 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.

Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

Genome Center, University of California, Davis, Davis, California, USA.

School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

Department of Biosciences, University of Milano, Milan, Italy.

IBBA-CNR Unit of Milano, Institute of Agricultural Biology and Biotechnology, Milan, Italy.

Department of Cell Biology, New York University School of Medicine, New York, New York, USA.

Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.

The University of Birmingham, Birmingham, UK.

Department of Microbiology, New York University School of Medicine, New York, New York, USA.

Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK.

Department of Biological Chemistry, Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

Department of Chemistry, Bielefeld University, Bielefeld, Germany.

Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.

Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia.

Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.

ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, Australia.

Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.

Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia.

Max Planck Institute for Biology, Tübingen, Germany.

Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.

Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK.

Department of Biomedicine, University of Bergen, Bergen, Norway.

Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.

ISPA-CNR Unit of Lecce, Institute of Sciences of Food Production, Lecce, Italy.

Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA.

California NanoSystems Institute, University of California, Los Angeles, California, USA.

Lanzhou University School of Life Sciences, Lanzhou, China.

Department of Biosciences, Rice University, Houston, Texas, USA.

Department of Microbiology-Immunology, Northwestern Feinberg School of Medicine, Chicago, Illinois, USA.

NanoTag Biotechnologies GmbH, Göttingen, Germany.

Institute of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Göttingen, Germany.

Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, Göttingen, Germany.

Department of Chemistry, Rice University, Houston, Texas, USA.

Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska, USA.

Department of Bioengineering, Rice University, Houston, Texas, USA.

University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.

Centre for Structural Systems Biology, Leibniz-Institut für Virologie (LIV), Hamburg, Germany.

Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA.

Macromolecule Content

Total Structure Weight: 38.26 kDa
Atom Count: 2,644
Modeled Residue Count: 331
Deposited Residue Count: 350
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF2807 domain-containing protein	A, B	175	Bdellovibrio bacteriovorus HD100	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6MN62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]