4WU2 | pdb_00004wu2

Structure of the PTP-like myo-inositol phosphatase from Selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate

• PDB DOI: https://doi.org/10.2210/pdb4WU2/pdb

• Classification: HYDROLASE
• Organism(s): Selenomonas ruminantium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-10-30 Released: 2015-11-04 
• Deposition Author(s): Bruder, L.M., Mosimann, S.C.
• Funding Organization(s): Canada Foundation for Innovation, Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate

Bruder, L.M.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.69 kDa 
• Atom Count: 5,705 
• Modeled Residue Count: 626 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myo-inositol phosphohydrolase	A, B	342	Selenomonas ruminantium	Mutation(s): 1  Gene Names: phyA EC: 3.1.3.8
UniProt
Find proteins for Q7WUJ1 (Selenomonas ruminantium) Explore Q7WUJ1  Go to UniProtKB:  Q7WUJ1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I3P	C [auth A], G [auth B]	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE C6 H15 O15 P3 MMWCIQZXVOZEGG-XJTPDSDZSA-N
PO4	D [auth A], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], F [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.98	α = 90
b = 137.67	β = 102.42
c = 80.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Bruder, L.M., Mosimann, S.C.

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

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description