7QEH

LTA-binding domain of SlpA, the S-layer protein from Lactobacillus amylovorus

PDB DOI: https://doi.org/10.2210/pdb7QEH/pdb

Classification: CELL ADHESION
Organism(s): Lactobacillus amylovorus GRL 1112
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-12-03 Released: 2022-12-14
Deposition Author(s): Eder, M., Dordic, A., Sagmeister, T., Pavkov-Keller, T.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.190
R-Value Work: 0.163
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The binding of the lactobacilli S-layer protein to the bacterial cell through interaction with LTA

Eder, M., Gubensaek, N., Sagmeister, T., Grininger, C., Vejzovic, D., Damisch, E., Dordic, A., Codee, J., Pavkov-Keller, T.

To be published.

Macromolecule Content

Total Structure Weight: 16.33 kDa
Atom Count: 1,053
Modelled Residue Count: 123
Deposited Residue Count: 144
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-layer	A	144	Lactobacillus amylovorus GRL 1112	Mutation(s): 0 Gene Names: LA2_00970
UniProt
Find proteins for E4SK47 (Lactobacillus amylovorus (strain GRL 1112)) Explore E4SK47 Go to UniProtKB: E4SK47
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E4SK47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.190
R-Value Work: 0.163
R-Value Observed: 0.166
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.561	α = 90
b = 43.481	β = 90
c = 89.107	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SHELXCD	phasing
SHELXE	model building
PHENIX	refinement
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-12-14

Deposition Author(s):

Pavkov-Keller, T.

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P29432

Revision History (Full details and data files)

Version 1.0: 2022-12-14
Type: Initial release

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 R01GM133198.