5J16 | pdb_00005j16

Crystal structure of Inositol monophosphate bound SaIMPase-II

• PDB DOI: https://doi.org/10.2210/pdb5J16/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus MSSA476
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-29 Released: 2017-02-08 
• Deposition Author(s): Dutta, A., Bhattacharyya, S., Das, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.237 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Inositol monophosphate bound SaIMPase-II

Dutta, A., Bhattacharyya, S., Das, A.K.

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 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 127.03 kDa 
• Atom Count: 7,985 
• Modeled Residue Count: 1,019 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol monophosphatase family protein	A, B, C, D	283	Staphylococcus aureus subsp. aureus MSSA476	Mutation(s): 0  Gene Names: SAS1042
UniProt
Find proteins for A0A1I9GET0 (Staphylococcus aureus (strain MSSA476)) Explore A0A1I9GET0  Go to UniProtKB:  A0A1I9GET0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPD	G [auth A], J [auth B], M [auth C]	D-MYO-INOSITOL-1-PHOSPHATE C6 H11 O9 P INAPMGSXUVUWAF-UOTPTPDRSA-L
PO4	P [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], N [auth D], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.237 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.942	α = 105.46
b = 78.762	β = 102.28
c = 80.052	γ = 109.47

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Dutta, A., Bhattacharyya, S., Das, A.K.

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description