7K67 | pdb_00007k67

Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus

PDB DOI: https://doi.org/10.2210/pdb7K67/pdb

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

Deposited: 2020-09-18 Released: 2021-11-10
Deposition Author(s): Cleland, C.P., Van Herk, P.H., Mosimann, S.C.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.170 (Depositor), 0.174 (DCC)
R-Value Work:
0.156 (Depositor), 0.157 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus

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

To be published.

Macromolecule Content

Total Structure Weight: 132.85 kDa
Atom Count: 9,940
Modeled Residue Count: 1,098
Deposited Residue Count: 1,240
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4XPJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], M [auth D]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C]	K [auth C], N [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.170 (Depositor), 0.174 (DCC)
R-Value Work: 0.156 (Depositor), 0.157 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.009	α = 90
b = 97.32	β = 92.29
c = 104.1	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-11-10

Deposition Author(s):

Cleland, C.P.

Van Herk, P.H.

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, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2023-10-18
Changes: Data collection, Refinement description