8V9V | pdb_00008v9v

Yeh-like adhesin YhlD receptor binding domain

PDB DOI: https://doi.org/10.2210/pdb8V9V/pdb

Classification: CELL ADHESION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-10 Released: 2025-06-11
Deposition Author(s): Lopatto, E.D.B., Tamadonfar, K.O., Klein, R.D., Hultgren, S.J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.263 (Depositor), 0.262 (DCC)
R-Value Work:
0.224 (Depositor), 0.220 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Yeh-like adhesin YhlD receptor binding domain

Lopatto, E.D.B., Tamadonfar, K.O., Klein, R.D., Hultgren, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 19.2 kDa
Atom Count: 1,262
Modeled Residue Count: 167
Deposited Residue Count: 176
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pilus assembly protein	A	176	Escherichia coli	Mutation(s): 0 Gene Names: C9E67_10040, NCTC13127_02335
UniProt
Find proteins for Q8X7F4 (Escherichia coli O157:H7) Explore Q8X7F4 Go to UniProtKB: Q8X7F4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8X7F4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.263 (Depositor), 0.262 (DCC)
R-Value Work: 0.224 (Depositor), 0.220 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.302	α = 90
b = 104.117	β = 90
c = 131.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

Lopatto, E.D.B.

Tamadonfar, K.O.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-06-11
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.