9N58 | pdb_00009n58

Structure of the PTP-like myo-inositol phosphatase from Solidesulfovibrio magneticus in complex with myo-inositol hexakisphosphate

• PDB DOI: https://doi.org/10.2210/pdb9N58/pdb
• Entry: 9N58 supersedes: 7K6W

• Classification: HYDROLASE
• Organism(s): Solidesulfovibrio magneticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-02-03 Released: 2025-02-12 
• Deposition Author(s): Cleland, C.P., Mosimann, S.C.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Novel Structure of PhyA from Solidesulfovibrio magneticus indicates the phosphate-binding loop influences InsP6 binding modes and substrate specificity

Cleland, C.P., Mosimann, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 133.98 kDa 
• Atom Count: 9,551 
• Modeled Residue Count: 1,087 
• Deposited Residue Count: 1,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine specific protein phosphatases domain-containing protein	A, B, C, D	310	Solidesulfovibrio magneticus	Mutation(s): 1  Gene Names: DMR_16880
UniProt
Find proteins for C4XPJ9 (Solidesulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1)) Explore C4XPJ9  Go to UniProtKB:  C4XPJ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.019	α = 90
b = 97.339	β = 92.583
c = 104.055	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Cleland, C.P., Mosimann, S.C.
• This entry supersedes: 7K6W

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

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release