8VC9 | pdb_00008vc9

Crystal structure of Rec-controlled histidine kinase LvrB, BeF3-activated

PDB DOI: https://doi.org/10.2210/pdb8VC9/pdb

Classification: SIGNALING PROTEIN
Organism(s): Leptospira interrogans serovar Copenhageni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-13 Released: 2024-12-18
Deposition Author(s): Mechaly, A., Buschiazzo, A.
Funding Organization(s): Agencia Nacional de Investigacion e Innovacion (ANII)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Coiled coil formation and symmetry breaking activates the Leptospira virulence regulator LvrB, a hybrid response regulator

Agustoni, E., Mechaly, A., Dalla Rizza, J., Isaikina, P., Trajtenberg, F., Muntener, T., Wunder, E., Ko, A.I., Schirmer, T., Buschiazzo, A., Hiller, S.

To be published.

Macromolecule Content

Total Structure Weight: 264.66 kDa
Atom Count: 18,135
Modeled Residue Count: 2,265
Deposited Residue Count: 2,292
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leptospira virulence regulator B (LvrB)	A, B, C, D, E A, B, C, D, E, F	382	Leptospira interrogans serovar Copenhageni	Mutation(s): 0 Gene Names: lic11708 EC: 2.7.13.3
UniProt
Find proteins for Q8F424 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)) Explore Q8F424 Go to UniProtKB: Q8F424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8F424
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACP (Subject of Investigation/LOI) Query on ACP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth C] SDF format, chain X [auth E] SDF format, chain T [auth D] SDF format, chain L [auth B] SDF format, chain EA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain X [auth E] MOL2 format, chain T [auth D] MOL2 format, chain L [auth B] MOL2 format, chain EA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain P [auth C] mmCIF format, chain X [auth E] mmCIF format, chain T [auth D] mmCIF format, chain L [auth B] mmCIF format, chain EA [auth F]	EA [auth F] G [auth A] L [auth B] P [auth C] T [auth D] EA [auth F], G [auth A], L [auth B], P [auth C], T [auth D], X [auth E]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain EA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain EA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain K [auth A] SDF format, chain DA [auth E] SDF format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain BA [auth E]	BA [auth E], CA [auth E], DA [auth E], K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain K [auth A] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain K [auth A]
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain GA [auth F] SDF format, chain N [auth B] SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain I [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain I [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain I [auth A]	GA [auth F] I [auth A] N [auth B] R [auth C] V [auth D] GA [auth F], I [auth A], N [auth B], R [auth C], V [auth D], Z [auth E]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain GA [auth F] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain GA [auth F] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain HA [auth F] SDF format, chain AA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain HA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain HA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] FA [auth F] H [auth A] HA [auth F] J [auth A] AA [auth E], FA [auth F], H [auth A], HA [auth F], J [auth A], M [auth B], O [auth B], Q [auth C], S [auth C], U [auth D], W [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth D] Focus chain Y [auth E]