2ODJ

Crystal structure of the outer membrane protein OprD from Pseudomonas aeruginosa

Structural Biology Knowledgebase: 2ODJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.315
  • R-Value Work: 0.248

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ODJ

Classification: MEMBRANE PROTEIN

Total Structure Weight: 97340.41

Macromolecule Entities
Molecule Chains Length Organism Details
Porin D A, B 428 Pseudomonas aeruginosa EC#: 3.4.21 IUBMB
Mutation: M88M, M112M, M118M, M335M, M349M
Gene Name(s): oprD PA0958
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: BETA-BARREL

Subgroup Name: Outer Membrane Carboxylate Channels (Occ)

Protein Name: OccD1 (OprD) basic amino acid uptake channel


Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C8E
Query on C8E

A, B (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.315
  • R-Value Work: 0.248
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 111.37 α = 90.00
b = 97.53 β = 119.63
c = 95.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

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

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4