8OKH

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

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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 

Literature

title to be confirmed

Caulton, S.G., Lovering, A.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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 = 90.159	α = 90
b = 90.159	β = 90
c = 112.552	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Caulton, S.G., Lovering, A.L.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	209437/Z/17/Z

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release