9Y0P | pdb_00009y0p

Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode I

• PDB DOI: https://doi.org/10.2210/pdb9Y0P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12, Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-08-28 Released: 2026-03-25 
• Deposition Author(s): Cunliffe, T.R., Heras, B., Paxman, J.J.
• Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

The Cis-Proline Lock, A Conserved Scaffold for Catalysis in Thioredoxin-Fold Oxidoreductases

Cunliffe, T.R., Wang, G., Penning, S., Subedi, P., Totsika, M., Paxman, J.J., Heras, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.6 kDa 
• Atom Count: 3,623 
• Modeled Residue Count: 399 
• Deposited Residue Count: 408 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbA	A, B [auth C]	190	Escherichia coli K-12	Mutation(s): 1  Gene Names: dsbA, dsf, ppfA, b3860, JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12)) Explore P0AEG4  Go to UniProtKB:  P0AEG4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from LPS-assembly protein LptD	C [auth D], D [auth B]	14	Escherichia coli	Mutation(s): 2
UniProt
Find proteins for P31554 (Escherichia coli (strain K12)) Explore P31554  Go to UniProtKB:  P31554

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3	F [auth A], G [auth A], J [auth A], K [auth C], M [auth C]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.21	α = 90
b = 79.335	β = 90
c = 82.503	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Cunliffe, T.R., Heras, B., Paxman, J.J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP190101613
Australian Research Council (ARC)	Australia	DP210100673
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1144046

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release