9DIV | pdb_00009div

The crystal structure of de novo designed ChuA binding protein C8

PDB DOI: https://doi.org/10.2210/pdb9DIV/pdb

Classification: TRANSPORT PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-06 Released: 2025-05-21
Deposition Author(s): Fox, D., Grinter, R.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 ?
R-Value Free:
0.324 (Depositor), 0.337 (DCC)
R-Value Work:
0.301 (Depositor), 0.314 (DCC)
R-Value Observed:
0.302 (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

Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins

Fox, D.R., Asadollahi, K., Samuels, I., Spicer, B.A., Kropp, A., Lupton, C.J., Lim, K., Wang, C., Venugopal, H., Dramicanin, M., Knott, G.J., Grinter, R.

(2025) Nat Commun

Macromolecule Content

Total Structure Weight: 122.71 kDa
Atom Count: 7,525
Modeled Residue Count: 1,082
Deposited Residue Count: 1,216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed ChuA binding protein C8	A, B, C, D, E A, B, C, D, E, F, G, H	152	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: 2.46 ?
R-Value Free: 0.324 (Depositor), 0.337 (DCC)
R-Value Work: 0.301 (Depositor), 0.314 (DCC)
R-Value Observed: 0.302 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 85.366	α = 90
b = 110.3	β = 90
c = 127.338	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1197376
Australian Research Council (ARC)	Australia	LE200100045, LE120100090

Revision History (Full details and data files)

Version 1.0: 2025-05-21
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.