5UBK | pdb_00005ubk

Inactive S1A/N269D-cpPvdQ mutant in complex with the pyoverdine precursor PVDIq reveals a specific binding pocket for the D-Tyr of this substrate

• PDB DOI: https://doi.org/10.2210/pdb5UBK/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-12-20 Released: 2017-03-01 
• Deposition Author(s): Mascarenhas, R., Catlin, D., Wu, R., Clevenger, K., Fast, W., Liu, D.
• Funding Organization(s): National Science Foundation (NSF, United States), Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Circular Permutation Reveals a Chromophore Precursor Binding Pocket of the Siderophore Tailoring Enzyme PvdQ

Mascarenhas, R., Clevenger, K., Catlin, D., Wu, R., Fast, W., Liu, D.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 78.84 kDa 
• Atom Count: 5,695 
• Modeled Residue Count: 709 
• Deposited Residue Count: 709 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-homoserine lactone acylase PvdQ	A	709	Pseudomonas aeruginosa	Mutation(s): 2  Gene Names: pvdQ EC: 3.5.1.97
UniProt
Find proteins for Q9I194 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I194  Go to UniProtKB:  Q9I194

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
83M	B [auth A]	N-[(1R)-1-{(6S)-6-[(2-amino-2-oxoethyl)carbamoyl]-1,4,5,6-tetrahydropyrimidin-2-yl}-2-(4-hydroxyphenyl)ethyl]-N~2~-tetradecanoyl-L-glutamine C34 H54 N6 O7 DGAYEIHJKULBKL-HZFUHODCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.384	α = 90
b = 168.361	β = 90
c = 93.643	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Mascarenhas, R., Catlin, D., Wu, R., Clevenger, K., Fast, W., Liu, D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1308672
Robert A. Welch Foundation	United States	F-1572

Revision History  

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary