5UBK

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.237
R-Value Work: 0.184
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I194
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
83M Query on 83M Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.237
R-Value Work: 0.184
R-Value Observed: 0.187
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-01

Deposition Author(s):

Mascarenhas, R.

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 (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.