7SDD | pdb_00007sdd

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), 0.207 (DCC)
R-Value Work:
0.181 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 288
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZRR1
Sequence Annotations Expand
Reference Sequence

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), 0.207 (DCC)
R-Value Work: 0.181 (Depositor), 0.182 (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

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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

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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.