8A0X | pdb_00008a0x

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
Deposition Author(s): Hadzi, S., Loris, R.
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 (Depositor), 0.270 (DCC)
R-Value Work:
0.238 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Fuzzy DNA recognition by a prokaryotic transcription factor

Hadzi, S., Loris, R.

To be published.

Macromolecule Content

Total Structure Weight: 69.09 kDa
Atom Count: 4,539
Modeled Residue Count: 485
Deposited Residue Count: 494
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin HigA-2	A, B	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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin HigB-2	C, D	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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (30-MER)	E	31	Vibrio cholerae
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	F	31	Vibrio cholerae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth F] SDF format, chain N [auth F] SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain I [auth A]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth D] G [auth A], H [auth A], I [auth A], J [auth B], K [auth D], L [auth E], M [auth F], N [auth F], O [auth F], P [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth F]