6R1G | pdb_00006r1g

Crystal structure of Borrelia burgdorferi periplasmic protein BB0365 (IPLA7, p22)

PDB DOI: https://doi.org/10.2210/pdb6R1G/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Borreliella burgdorferi B31
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-03-14 Released: 2019-09-18
Deposition Author(s): Brangulis, K., Akopjana, I., Petrovskis, I., Kazaks, A., Tars, K.
Funding Organization(s): European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.192 (Depositor), 0.200 (DCC)
R-Value Work:
0.175 (Depositor), 0.190 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural analysis of Borrelia burgdorferi periplasmic lipoprotein BB0365 involved in Lyme disease infection.

Brangulis, K., Akopjana, I., Petrovskis, I., Kazaks, A., Jekabsons, A., Jaudzems, K., Viksna, A., Bertins, M., Tars, K.

(2020) FEBS Lett 594: 317-326

PubMed: 31486526 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13594
Primary Citation of Related Structures:
6R1G

PubMed Abstract:
The periplasmic lipoprotein BB0365 of the Lyme disease agent Borrelia burgdorferi is expressed throughout mammalian infection and is essential for all phases of Lyme disease infection; its function, however, remains unknown. In the current study, our structural analysis of BB0365 revealed the same structural fold as that found in the NqrC and RnfG subunits of the NADH:quinone and ferredoxin:NAD ⁺ sodium-translocating oxidoreductase complexes, which points to a potential role for BB0365 as a component of the sodium pump. Additionally, BB0365 coordinated Zn ²⁺ by the His51, His55, His140 residues, and the Zn ²⁺ -binding site indicates that BB0365 could act as a potential metalloenzyme; therefore, this structure narrows down the potential functions of BB0365, an essential protein for B. burgdorferi to cause Lyme disease.

Organizational Affiliation

Latvian Biomedical Research and Study Centre, Riga, Latvia.

Macromolecule Content

Total Structure Weight: 39.09 kDa
Atom Count: 2,597
Modeled Residue Count: 296
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer surface 22 kDa lipoprotein	A, B	171	Borreliella burgdorferi B31	Mutation(s): 0 Gene Names: p22, BB_0365
UniProt
Find proteins for P0CL67 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore P0CL67 Go to UniProtKB: P0CL67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CL67
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B], I [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.192 (Depositor), 0.200 (DCC)
R-Value Work: 0.175 (Depositor), 0.190 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.65	α = 90
b = 63.47	β = 111.34
c = 61.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	data scaling
SHELXCD	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Funding Organization	Location	Grant Number
European Regional Development Fund	Latvia	1.1.1.2/VIAA/1/16/144

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2020-02-05
Changes: Database references
Version 1.2: 2024-05-15
Changes: Data collection, Database references, Derived calculations