3E9Z | pdb_00003e9z

Crystal structure of purine nucleoside phosphorylase from Schistosoma mansoni in complex with 6-chloroguanine

• PDB DOI: https://doi.org/10.2210/pdb3E9Z/pdb

• Classification: TRANSFERASE
• Organism(s): Schistosoma mansoni
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-24 Released: 2009-09-01 
• Deposition Author(s): Pereira, H.M., Rezende, M.M., Oliva, G., Garratt, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase (SmPNP) in complex with adenine, 8-aminoguanine, 8-azaguanine and 6-chloroguanine.

Pereira, H.M., Rezende, M.M., Oliva, G., Garratt, R.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 94.59 kDa 
• Atom Count: 7,055 
• Modeled Residue Count: 833 
• Deposited Residue Count: 861 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine-nucleoside phosphorylase	A, B, C	287	Schistosoma mansoni	Mutation(s): 0  Gene Names: SmPNP EC: 2.4.2.1
UniProt
Find proteins for Q9BMI9 (Schistosoma mansoni) Explore Q9BMI9  Go to UniProtKB:  Q9BMI9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6GU	F [auth A], L [auth C]	6-chloroguanine C5 H4 Cl N5 RYYIULNRIVUMTQ-UHFFFAOYSA-N
SO4	E [auth A], J [auth B], M [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	D [auth A], G [auth A], H [auth B], K [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.821	α = 90
b = 118.121	β = 90
c = 129.055	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Pereira, H.M., Rezende, M.M., Oliva, G., Garratt, R.C.

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description