2ODJ

Crystal structure of the outer membrane protein OprD from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb2ODJ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2006-12-22 Released: 2007-10-16 
• Deposition Author(s): Biswas, S., van den Berg, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.315 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 

Literature

Structural insight into OprD substrate specificity.

Biswas, S., Mohammad, M.M., Patel, D.R., Movileanu, L., van den Berg, B.

(2007) Nat Struct Mol Biol 14: 1108-1109

• PubMed: 17952093 
• DOI: https://doi.org/10.1038/nsmb1304
• Primary Citation of Related Structures:  
  2ODJ


• PubMed Abstract: 
  

  OprD proteins form a large family of substrate-specific outer-membrane channels in Gram-negative bacteria. We report here the X-ray crystal structure of OprD from Pseudomonas aeruginosa, which reveals a monomeric 18-stranded beta-barrel characterized by a very narrow pore constriction, with a positively charged basic ladder on one side and an electronegative pocket on the other side. The location of highly conserved residues in OprD suggests that the structure represents the general architecture of OprD channels.

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Organizational Affiliation: 

Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 97.34 kDa 
• Atom Count: 6,199 
• Modelled Residue Count: 770 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Porin D	A, B	428	Pseudomonas aeruginosa PAO1	Mutation(s): 5  Gene Names: oprD EC: 3.4.21 Membrane Entity: Yes
UniProt
Find proteins for P32722 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P32722  Go to UniProtKB:  P32722

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.315 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.37	α = 90
b = 97.525	β = 119.63
c = 95.788	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Biswas, S., van den Berg, B.

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations