7SDD

Structure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate

PDB DOI: https://doi.org/10.2210/pdb7SDD/pdb

Classification: HYDROLASE
Organism(s): Legionella pneumophila str. Paris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-09-29 Released: 2022-10-19
Deposition Author(s): Cleland, C.P., Mosimann, S.C.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate

Cleland, C.P., Mosimann, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 36.53 kDa
Atom Count: 2,845
Modelled Residue Count: 288
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myo-inositol phosphohydrolase	A	314	Legionella pneumophila str. Paris	Mutation(s): 1 Gene Names: hopD2, NCTC12000_03020 EC: 3.1.3.48
UniProt
Find proteins for Q5ZRR1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRR1 Go to UniProtKB: Q5ZRR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZRR1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4IP (Subject of Investigation/LOI) Query on 4IP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE C₆ H₁₆ O₁₈ P₄ CIPFCGZLFXVXBG-CNWJWELYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.581	α = 90
b = 63.211	β = 90
c = 95.237	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-10-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2022-10-19
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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.