8X7N | pdb_00008x7n

Cell-cell adhesion Nanobody/Antigen Pair

PDB DOI: https://doi.org/10.2210/pdb8X7N/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, synthetic construct
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2023-11-24 Released: 2024-07-17
Deposition Author(s): Chen, P.-P., Hsia, K.-C., Ting, S.-Y., Chen, Y.-C.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.67 Å
R-Value Free:
0.285 (Depositor), 0.290 (DCC)
R-Value Work:
0.260 (Depositor), 0.260 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

A whole-cell screening platform for discovery cell adhesion molecules enabling programmable bacterial cell-cell adhesion

Chen, P.-P., Hsia, K.-C., Ting, S.-Y., Chen, Y.-C.

To be published.

Macromolecule Content

Total Structure Weight: 139.05 kDa
Atom Count: 8,930
Modeled Residue Count: 1,190
Deposited Residue Count: 1,290
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conjugative transfer: aggregate stability	A, C, E, G, I	135	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: traN
UniProt
Find proteins for Q93GM7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q93GM7 Go to UniProtKB: Q93GM7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93GM7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb-TraN	B, D, F, H, J	123	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.67 Å
R-Value Free: 0.285 (Depositor), 0.290 (DCC)
R-Value Work: 0.260 (Depositor), 0.260 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.864	α = 90
b = 153.263	β = 90
c = 163.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-IVA-112-L05

Revision History (Full details and data files)

Version 1.0: 2024-07-17
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary

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.