9DBH | pdb_00009dbh

Structure of Hailong HalB in complex with oligodeoxyadenylate

• PDB DOI: https://doi.org/10.2210/pdb9DBH/pdb

• Classification: ANTIVIRAL PROTEIN/DNA
• Organism(s): Rhodobacteraceae bacterium QY30, DNA molecule
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-23 Released: 2025-05-07 
• Deposition Author(s): Tan, J.M.J., Melamed, S., Cofsky, J.C., Hobbs, S.J., Kruse, A.C., Sorek, R., Kranzusch, P.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: in silico

Literature

Structure of HalB in complex with oligodeoxyadenylate

Tan, J.M.J., Melamed, S., Cofsky, J.C., Hobbs, S.J., Kruse, A.C., Sorek, R., Kranzusch, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 111.75 kDa 
• Atom Count: 7,719 
• Modelled Residue Count: 871 
• Deposited Residue Count: 966 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HalB	A, B, C, D	237	Rhodobacteraceae bacterium QY30	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')	E	6	DNA molecule

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')	F	5	DNA molecule

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')	G	4	DNA molecule

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')	H	3	DNA molecule

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	I [auth B], J [auth C], K [auth D], L [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.365	α = 90
b = 133.269	β = 107.92
c = 79.165	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Tan, J.M.J., Melamed, S., Cofsky, J.C., Hobbs, S.J., Kruse, A.C., Sorek, R., Kranzusch, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1DP2GM146250

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release