Download MendeleyStructure 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.
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
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.88 ?
- 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
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HalB | 237 | Rhodobacteraceae bacterium QY30 | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3') | 6 | DNA molecule |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3') | 5 | DNA molecule |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3') | 4 | DNA molecule |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3') | 3 | DNA molecule |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MN (Subject of Investigation/LOI) Query on MN | 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 ?
- 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 ( ? ) | Angle ( ? ) |
|---|---|
| a = 56.365 | ¦Á = 90 |
| b = 133.269 | ¦Â = 107.92 |
| c = 79.165 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
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.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | 1DP2GM146250 |
Revision History (Full details and data files)
- Version 1.0: 2025-05-07
Type: Initial release
