4AS5 | pdb_00004as5

Structure of mouse inositol monophosphatase 1

PDB DOI: https://doi.org/10.2210/pdb4AS5/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-27 Released: 2012-10-10
Deposition Author(s): Singh, N., Knight, M., Halliday, A.C., Lack, N.A., Lowe, E.D., Churchill, G.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.214 (Depositor), 0.202 (DCC)
R-Value Work:
0.160 (Depositor)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Cloning, Expression, Purification, Crystallization and X-Ray Analysis of Inositol Monophosphatase from Mus Musculus and Homo Sapiens.

Singh, N., Halliday, A.C., Knight, M., Lack, N.A., Lowe, E.D., Churchill, G.C.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1149

PubMed: 23027737 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309112035191
Primary Citation Related Structures:
4AS4, 4AS5

PubMed Abstract:
Inositol monophosphatase (IMPase) catalyses the hydrolysis of inositol monophosphate to inositol and is crucial in the phosphatidylinositol (PI) signalling pathway. Lithium, which is the drug of choice for bipolar disorder, inhibits IMPase at therapeutically relevant plasma concentrations. Both mouse IMPase 1 (MmIMPase 1) and human IMPase 1 (HsIMPase 1) were cloned into pRSET5a, expressed in Escherichia coli, purified and crystallized using the sitting-drop method. The structures were solved at resolutions of 2.4 and 1.7 Å, respectively. Comparison of MmIMPase 1 and HsIMPase 1 revealed a core r.m.s. deviation of 0.516 Å.

Organizational Affiliation

Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, England.

Macromolecule Content

Total Structure Weight: 124.15 kDa
Atom Count: 9,300
Modeled Residue Count: 1,096
Deposited Residue Count: 1,108
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INOSITOL MONOPHOSPHATASE 1	A, B, C, D	277	Mus musculus	Mutation(s): 0 EC: 3.1.3.25 (PDB Primary Data), 3.1.3.94 (UniProt)
UniProt
Find proteins for O55023 (Mus musculus) Explore O55023 Go to UniProtKB: O55023
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55023
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Z [auth C] SDF format, chain I [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain I [auth A]	AA [auth C] GA [auth D] HA [auth D] I [auth A] IA [auth D] AA [auth C], GA [auth D], HA [auth D], I [auth A], IA [auth D], J [auth A], R [auth B], S [auth B], Z [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain V [auth C] SDF format, chain CA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] MOL2 format, chain CA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C] mmCIF format, chain CA [auth D]	CA [auth D], E [auth A], N [auth B], V [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	T [auth B], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain T [auth B] Focus chain U [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	BA [auth C], JA [auth D], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain BA [auth C] Focus chain JA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain F [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain F [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain F [auth A]	DA [auth D] EA [auth D] F [auth A] FA [auth D] G [auth A] DA [auth D], EA [auth D], F [auth A], FA [auth D], G [auth A], H [auth A], O [auth B], P [auth B], Q [auth B], W [auth C], X [auth C], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.214 (Depositor), 0.202 (DCC)
R-Value Work: 0.160 (Depositor)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.785	α = 90
b = 81.49	β = 113.77
c = 97.139	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2012-10-17
Changes: Database references
Version 1.2: 2012-12-26
Changes: Database references, Derived calculations, Other, Refinement description, Structure summary
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description