7CBS | pdb_00007cbs

Crystal structure of SpaB basal pilin from Lactobacillus rhamnosus GG

PDB DOI: https://doi.org/10.2210/pdb7CBS/pdb

Classification: CELL ADHESION
Organism(s): Lacticaseibacillus rhamnosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-13 Released: 2020-12-30
Deposition Author(s): Megta, A.K., Pratap, S., Kant, A., Krishnan, V.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.228 (Depositor), 0.234 (DCC)
R-Value Work:
0.190 (Depositor), 0.196 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7CBS

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

Literature

Crystal structure of the atypically adhesive SpaB basal pilus subunit: Mechanistic insights about its incorporation in lactobacillar SpaCBA pili.

Megta, A.K., Pratap, S., Kant, A., Palva, A., von Ossowski, I., Krishnan, V.

(2020) Curr Res Struct Biol 2: 229-238

DOI: https://doi.org/10.1016/j.crstbi.2020.11.001

Macromolecule Content

Total Structure Weight: 151.24 kDa
Atom Count: 7,270
Modeled Residue Count: 991
Deposited Residue Count: 1,400
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPXTG cell wall anchor domain-containing protein	A B C D E A, B, C, D, E, F [auth G], G [auth F], H [auth L]	175	Lacticaseibacillus rhamnosus	Mutation(s): 0 Gene Names: F8M46_02260

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B]	J [auth B], L [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth L] SDF format, chain N [auth F] SDF format, chain K [auth C] SDF format, chain I [auth A] MOL2 format, chain O [auth L] MOL2 format, chain N [auth F] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] mmCIF format, chain O [auth L] mmCIF format, chain N [auth F] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A]	I [auth A], K [auth C], N [auth F], O [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain N [auth F] Focus chain O [auth L] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain N [auth F] Focus chain O [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.228 (Depositor), 0.234 (DCC)
R-Value Work: 0.190 (Depositor), 0.196 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.526	α = 90
b = 51.526	β = 90
c = 408.208	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR5891/BRB/10/1098/2012

Revision History (Full details and data files)

Version 1.0: 2020-12-30
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.