2Y2X | pdb_00002y2x

Crystal Structure of Pseudomonas Aeruginosa OpdK with Vanillate

• PDB DOI: https://doi.org/10.2210/pdb2Y2X/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2010-12-16 Released: 2011-12-28 
• Deposition Author(s): Touw, D.S., Vijayaraghavan, J., Vandenberg, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Pseudomonas Aeruginosa Opdk with Vanillate

Touw, D.S., Vijayaraghavan, J., Vandenberg, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.79 kDa 
• Atom Count: 6,878 
• Modeled Residue Count: 752 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VANILLATE PORIN OPDK	A, B	390	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9HUR5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUR5  Go to UniProtKB:  Q9HUR5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E	AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
VNL	LA [auth B], MA [auth B], R [auth A], S [auth A]	4-HYDROXY-3-METHOXYBENZOATE C8 H7 O4 WKOLLVMJNQIZCI-UHFFFAOYSA-M
EDO	C [auth A], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.142	α = 90
b = 96.84	β = 90
c = 121.557	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Touw, D.S., Vijayaraghavan, J., Vandenberg, B.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description