6FG5 | pdb_00006fg5

Schistosoma mansoni Phosphodiesterase 4A

• PDB DOI: https://doi.org/10.2210/pdb6FG5/pdb

• Classification: HYDROLASE
• Organism(s): Schistosoma mansoni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-10 Released: 2019-01-30 
• Deposition Author(s): Brown, D.G., Schroeder, S., Gil, C.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.245 (Depositor) 
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

The structure of Schistosoma mansoni Phosphodiesterase 4A

Brown, D.G., Schroeder, S., Gil, C., Munday, J., Koning, H., Siderius, M., Leurs, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 84.8 kDa 
• Atom Count: 5,411 
• Modeled Residue Count: 659 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphodiesterase	A, B	370	Schistosoma mansoni	Mutation(s): 0  Gene Names: Smp_134140 EC: 3.1.4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.245 (Depositor) 
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.799	α = 90
b = 81.799	β = 90
c = 256.127	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MxCuBE	data collection
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Brown, D.G., Schroeder, S., Gil, C.

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Funding Organization	Location	Grant Number
European Union	United Kingdom	EC-FP7-602666-PDE4NPD

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description