7K6W

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

PDB DOI: https://doi.org/10.2210/pdb7K6W/pdb

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

Deposited: 2020-09-21 Released: 2021-11-10
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: 2.30 Å
R-Value Free: 0.220
R-Value Work: 0.196
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

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

Cleland, C.P., Van Herk, P.H., Mosimann, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 135.47 kDa
Atom Count: 8,995
Modelled Residue Count: 1,100
Deposited Residue Count: 1,240
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myo-inositol phosphohydrolase	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4XPJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D]	E [auth A], J [auth B], O [auth C], T [auth D]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D]	F [auth A], K [auth B], P [auth C], U [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	G [auth A] H [auth A] I [auth A] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], V [auth D], W [auth D], X [auth D], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.220
R-Value Work: 0.196
R-Value Observed: 0.196
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.839	α = 90
b = 95.989	β = 92.09
c = 103.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-10

Deposition Author(s):

Cleland, C.P.

Mosimann, S.C.

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

Revision History (Full details and data files)

Version 1.0: 2021-11-10
Type: Initial release
Version 2.0: 2021-11-24
Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2023-10-18
Changes: Data collection, Refinement description