7K6Y | pdb_00007k6y

Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus (high salt)

PDB DOI: https://doi.org/10.2210/pdb7K6Y/pdb

Classification: HYDROLASE
Organism(s): Solidesulfovibrio magneticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-21 Released: 2021-11-10
Deposition Author(s): Van Herk, P.H., 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: 1.75 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.190 (Depositor), 0.191 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

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 (high salt)

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

To be published.

Macromolecule Content

Total Structure Weight: 66.91 kDa
Atom Count: 4,652
Modeled Residue Count: 554
Deposited Residue Count: 620
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	310	Solidesulfovibrio magneticus	Mutation(s): 0 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.227 (Depositor), 0.228 (DCC)
R-Value Work: 0.190 (Depositor), 0.191 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.53	α = 90
b = 130.89	β = 90
c = 137.18	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-11-10

Deposition Author(s):

Van Herk, P.H.

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

7K6Y | pdb_00007k6y

Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus (high salt)

Literature

Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus (high salt)

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)