9QZ1 | pdb_00009qz1

MINPP1 from Bacteroides thetaiotaomicron E325N mutant complex with myo-inositol(1,2,4,5,6)pentaphosphate

• PDB DOI: https://doi.org/10.2210/pdb9QZ1/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-04-22 Released: 2025-06-11 
• Deposition Author(s): Li, A.W.H., Shang, X.Y., Hemmings, A.M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.265 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

A Structural Basis for the Stereospecificity of Multiple Inositol Polyphosphate Phosphatases

Salmon, M., Shang, X.Y., Li, A.W.H., Hemmings, A.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 100.12 kDa 
• Atom Count: 6,636 
• Modeled Residue Count: 787 
• Deposited Residue Count: 852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
multiple inositol polyphosphate histidine phosphatase 1	A, B	426	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1  Gene Names: BT_4744 EC: 3.1.3.62 (UniProt), 3.1.3.80 (UniProt)
UniProt
Find proteins for Q89YI8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89YI8  Go to UniProtKB:  Q89YI8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZNZ (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B]	(1R,2R,3R,4S,5R,6R)-6-hydroxycyclohexane-1,2,3,4,5-pentayl pentakis[dihydrogen (phosphate)] C6 H17 O21 P5 CTPQAXVNYGZUAJ-XCMZKKERSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.265 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.69	α = 90
b = 119.84	β = 108.07
c = 75.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Li, A.W.H., Shang, X.Y., Hemmings, A.M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M022978/1

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release