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 PDBTM MemProtMD

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.201 (Depositor), 0.201 (DCC)
R-Value Work:
0.180 (Depositor), 0.176 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Pseudomonas Aeruginosa Opdk with Vanillate

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

To be published.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HUR5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C8E Query on C8E Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain X [auth B] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain DA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B]	AA [auth B] BA [auth B] CA [auth B] D [auth A] DA [auth B] 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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
VNL Query on VNL Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	LA [auth B], MA [auth B], R [auth A], S [auth A]	4-HYDROXY-3-METHOXYBENZOATE C₈ H₇ O₄ WKOLLVMJNQIZCI-UHFFFAOYSA-M		Interactions Focus chain LA [auth B] Focus chain MA [auth B] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain LA [auth B] Focus chain MA [auth B] Focus chain R [auth A] Focus chain S [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain C [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain C [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain C [auth A]	C [auth A], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.201 (Depositor), 0.201 (DCC)
R-Value Work: 0.180 (Depositor), 0.176 (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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-12-28

Deposition Author(s):

Touw, D.S.

Vijayaraghavan, J.

Vandenberg, B.

Revision History (Full details and data files)

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