9QZ0 | pdb_00009qz0

MINPP1 from Bacteroides thetaiotaomicron E325N mutant complex with myo-inositol hexakisphosphate

PDB DOI: https://doi.org/10.2210/pdb9QZ0/pdb

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

Deposited: 2025-04-22 Released: 2025-05-14
Deposition Author(s): Li, A.W.H., Shang, X.Y., Hemmings, A.M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.193 (Depositor), 0.193 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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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.

Macromolecule Content

Total Structure Weight: 100.36 kDa
Atom Count: 7,282
Modeled Residue Count: 787
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
multiple inositol polyphosphate histidine phosphatase 1	A [auth AA], B [auth BA]	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89YI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP (Subject of Investigation/LOI) Query on IHP Download:Ideal Coordinates CCD File SDF format, chain E [auth BA] SDF format, chain D [auth AA] SDF format, chain C [auth AA] MOL2 format, chain E [auth BA] MOL2 format, chain D [auth AA] MOL2 format, chain C [auth AA] mmCIF format, chain E [auth BA] mmCIF format, chain D [auth AA] mmCIF format, chain C [auth AA]	C [auth AA], D [auth AA], E [auth BA]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain C [auth AA] Focus chain D [auth AA] Focus chain E [auth BA] Interactions & Density Focus chain C [auth AA] Focus chain D [auth AA] Focus chain E [auth BA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.193 (Depositor), 0.193 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.833	α = 90
b = 120.41	β = 108.04
c = 75.939	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	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: 2025-05-14

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

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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.