Download MendeleyFuzzy DNA recognition by a prokaryotic transcription factor
Hadzi, S., Loris, R.To be published.
8A0X
Crystal structure of the HigB2-HigA2 tetramer in complex with operator DNA
- PDB DOI: https://doi.org/10.2210/pdb8A0X/pdb
- NAKB: 8A0X
- Classification: DNA BINDING PROTEIN
- Organism(s): Vibrio cholerae
- Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): No
- Deposited: 2022-05-30 Released: 2023-05-03
- Funding Organization(s): Slovenian Research Agency, Research Foundation - Flanders (FWO)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.30 Å
- R-Value Free: 0.267
- R-Value Work: 0.238
- R-Value Observed: 0.239
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Antitoxin HigA-2 | 103 | Vibrio cholerae | Mutation(s): 0 Gene Names: higA-2, VC_A0469 |  | |
UniProt | |||||
Find proteins for Q9KMA5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KMA5 Go to UniProtKB: Q9KMA5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9KMA5 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Toxin HigB-2 | 113 | Vibrio cholerae | Mutation(s): 0 Gene Names: higB-2, VC_A0468 |  | |
UniProt | |||||
Find proteins for Q9KMA6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KMA6 Go to UniProtKB: Q9KMA6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9KMA6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (30-MER) | 31 | Vibrio cholerae |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (31-MER) | 31 | Vibrio cholerae |  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | G [auth A] H [auth A] I [auth A] J [auth B] K [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.30 Å
- R-Value Free: 0.267
- R-Value Work: 0.238
- R-Value Observed: 0.239
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 113.62 | α = 90 |
| b = 113.62 | β = 90 |
| c = 121.05 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| Slovenian Research Agency | Slovenia | P1-0201 |
| Research Foundation - Flanders (FWO) | Belgium | G003320N |
Revision History (Full details and data files)
- Version 1.0: 2023-05-03
Type: Initial release - Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
