9FZD

Structure of OmpA-long in complex with nanobody Nb39

PDB DOI: https://doi.org/10.2210/pdb9FZD/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli, Vicugna pacos
Expression System: Escherichia coli K-12
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2024-07-05 Released: 2024-07-17
Deposition Author(s): Ackle, F., Sorgenfrei, M., Seeger, M.A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.283
R-Value Work: 0.256
R-Value Observed: 0.257

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies

Sorgenfrei, M., Hurlimann, L.M., Printz, A., Wegner, F., Morger, D., Ackle, F., Remy, M.M., Montowski, G., Keserue, H., Cuenod, A., Imkamp, F., Egli, A., Keller, P.M., Seeger, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 32.47 kDa
Atom Count: 2,271
Modelled Residue Count: 294
Deposited Residue Count: 299
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein A	A	177	Escherichia coli	Mutation(s): 0 Gene Names: ompA, c1093 Membrane Entity: Yes
UniProt
Find proteins for A0A0H2V5V4 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2V5V4 Go to UniProtKB: A0A0H2V5V4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2V5V4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 39	B	122	Vicugna pacos	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: 2.30 Å
R-Value Free: 0.283
R-Value Work: 0.256
R-Value Observed: 0.257
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.398	α = 90
b = 52.572	β = 90
c = 256.746	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	407240_177368
Swiss National Science Foundation	Switzerland	PP00P3_170625

Revision History (Full details and data files)

Version 1.0: 2024-07-17
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.