8YKE | pdb_00008yke

Structure of two consecutively arrayed Rib domains (Rib8-9) from surface adhesin of Limosilactobacillus reuteri

PDB DOI: https://doi.org/10.2210/pdb8YKE/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Limosilactobacillus reuteri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-04 Released: 2025-03-05
Deposition Author(s): Xue, Y., Kang, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of two rib domains

Xue, Y., Kang, X.

To be published.

Macromolecule Content

Total Structure Weight: 16.56 kDa
Atom Count: 1,487
Modeled Residue Count: 154
Deposited Residue Count: 154
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YSIRK signal domain/LPXTG anchor domain surface protein	A	154	Limosilactobacillus reuteri	Mutation(s): 0 Gene Names: DB325_02015
UniProt
Find proteins for A0A2T5Q5G6 (Limosilactobacillus reuteri) Explore A0A2T5Q5G6 Go to UniProtKB: A0A2T5Q5G6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2T5Q5G6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.213 (Depositor), 0.214 (DCC)
R-Value Work: 0.164 (Depositor), 0.164 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.085	α = 90
b = 76.085	β = 90
c = 51.839	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data scaling
SADABS	data reduction
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-03-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22074070

Revision History (Full details and data files)

Version 1.0: 2025-03-05
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 R01GM157729.