5LTV | pdb_00005ltv

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 (Depositor), 0.220 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

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
Modeled 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] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth B] mmCIF format, chain W [auth D] mmCIF 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] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF 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] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF 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] mmCIF format, chain CA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth C] mmCIF 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 (Depositor), 0.220 (DCC)
R-Value Work: 0.177 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

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