8X4N | pdb_00008x4n

Crystal structure of the PI3P-binding domain of Legionella SetA in complex with inositol 1,3-bisphosphate

PDB DOI: https://doi.org/10.2210/pdb8X4N/pdb

Classification: TRANSFERASE
Organism(s): Legionella pneumophila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-15 Released: 2025-02-19
Deposition Author(s): Im, H.N., Lee, Y., Jang, D.M., Hahn, H., Kim, H.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.253 (Depositor), 0.264 (DCC)
R-Value Work:
0.205 (Depositor), 0.217 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the PI3P-binding domain of Legionella SetA in complex with inositol 1,3-bisphosphate

Im, H.N., Lee, Y., Jang, D.M., Hahn, H., Kim, H.S.

To be published.

Macromolecule Content

Total Structure Weight: 29.16 kDa
Atom Count: 1,847
Modeled Residue Count: 218
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subversion of eukaryotic traffic protein A	A, B	126	Legionella pneumophila	Mutation(s): 0 Gene Names: setA EC: 2.4.1
UniProt
Find proteins for Q5ZU30 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZU30 Go to UniProtKB: Q5ZU30
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZU30
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ITP (Subject of Investigation/LOI) Query on ITP Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER C₆ H₁₄ O₁₂ P₂ PUVHMWJJTITUGO-FICORBCRSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.253 (Depositor), 0.264 (DCC)
R-Value Work: 0.205 (Depositor), 0.217 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.247	α = 90
b = 36.915	β = 111.61
c = 72.407	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-02-19
Type: Initial release

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.