5LTV

LIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID CHEMORECPETOR PCTC IN COMPLEX WITH GABA

PDB DOI: https://doi.org/10.2210/pdb5LTV/pdb

Classification: SIGNALING PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-07 Released: 2017-09-20
Deposition Author(s): Gavira, J.A., Rico-Jimenez, M., Conejero-Muriel, M., Krell, T.
Funding Organization(s): MICINN

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.226
R-Value Work: 0.177
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

How Bacterial Chemoreceptors Evolve Novel Ligand Specificities

Gavira, J.A., Jimenez-Rico, M., Pineda-Molina, E., Krell, T.

(2020) mBio

DOI: https://doi.org/10.1128/mBio.03066-19

Macromolecule Content

Total Structure Weight: 210.38 kDa
Atom Count: 12,780
Modelled Residue Count: 1,516
Deposited Residue Count: 1,911
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemotactic transducer PctC	A, B, C, D, E A, B, C, D, E, F, G	273	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: PAMH19_3853
UniProt
Find proteins for Q9HW93 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HW93 Go to UniProtKB: Q9HW93
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HW93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ABU Query on ABU Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain P [auth B] SDF format, chain W [auth D] SDF format, chain Y [auth E] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E]	H [auth A], M [auth B], P [auth B], W [auth D], Y [auth E]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain W [auth D] Focus chain Y [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D]	AA [auth E] BA [auth E] DA [auth F] FA [auth G] GA [auth G] AA [auth E], BA [auth E], DA [auth F], FA [auth G], GA [auth G], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], U [auth C], V [auth C], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain L [auth A] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain L [auth A]	EA [auth F], HA [auth G], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain HA [auth G] Focus chain L [auth A] Interactions & Density Focus chain EA [auth F] Focus chain HA [auth G] Focus chain L [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth E]	CA [auth F] Q [auth B] R [auth B] S [auth B] T [auth C] CA [auth F], Q [auth B], R [auth B], S [auth B], T [auth C], Z [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.226
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.765	α = 90
b = 209.765	β = 90
c = 68.885	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Funding Organization	Location	Grant Number
MICINN	Spain	BIO2013-4297-P

Revision History (Full details and data files)

Version 1.0: 2017-09-20
Type: Initial release
Version 1.1: 2020-01-29
Changes: Database references, Structure summary
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references
Version 2.1: 2024-01-17
Changes: Refinement description