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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	L [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	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
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-10 
Deposition Author(s): Van Herk, P.H., Cleland, C.P., Mosimann, S.C.

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

Revision History  

• 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