6JNP | pdb_00006jnp

Structure of ExoT-SpcS Complex from Pseudomonas aeruginosa in 2.2 Angstrom

PDB DOI: https://doi.org/10.2210/pdb6JNP/pdb

Classification: TOXIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-17 Released: 2019-04-03
Deposition Author(s): Datta, S., Mondal, A.
Funding Organization(s): Council of Scientific & Industrial Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.254 (Depositor), 0.249 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of ExoT-SpcS Complex from Pseudomonas aeruginosa

Datta, S., Mondal, A.

To be published.

Macromolecule Content

Total Structure Weight: 65.3 kDa
Atom Count: 4,741
Modeled Residue Count: 578
Deposited Residue Count: 578
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exoenzyme T	A, D	57	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: yopE, NCTC13719_06179 EC: 2.4.2.31
UniProt
Find proteins for Q9I788 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I788 Go to UniProtKB: Q9I788
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I788
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CesT family type III secretion system chaperone	B, C, E, F	116	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: yerA
UniProt
Find proteins for G3XD93 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore G3XD93 Go to UniProtKB: G3XD93
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G3XD93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth E] SDF format, chain G [auth B] MOL2 format, chain H [auth E] MOL2 format, chain G [auth B] mmCIF format, chain H [auth E] mmCIF format, chain G [auth B]	G [auth B], H [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth E] Interactions & Density Focus chain G [auth B] Focus chain H [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.254 (Depositor), 0.249 (DCC)
R-Value Work: 0.211 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53	α = 90
b = 63	β = 98
c = 83	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research	India	TREAT- BSC0113, UNSEEN-BSC0116

Revision History (Full details and data files)

Version 1.0: 2019-04-03
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.