4PNP | pdb_00004pnp

THE HIGH RESOLUTION CRYSTAL STRUCTURE OF BOVINE SPLEEN PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX FORMS WITH PHOSPHATE AND 9-DEAZAINOSINE

• PDB DOI: https://doi.org/10.2210/pdb4PNP/pdb

• Classification: PHOSPHORYLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1998-03-30 Released: 1999-03-30 
• Deposition Author(s): Pugmire, M.J., Mao, C., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.248 (Depositor) 
• R-Value Work: 
  0.222 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

The High Resolution Crystal Structure of Bovine Spleen Purine Nucleoside Phosphorylase in Complex Forms with Phosphate and 9-Deazainosine

Pugmire, M.J., Mao, C., Ealick, S.E.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 32.1 kDa 
• Atom Count: 2,304 
• Modeled Residue Count: 284 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PURINE NUCLEOSIDE PHOSPHORYLASE	A	289	Bos taurus	Mutation(s): 0  EC: 2.4.2.1
UniProt
Find proteins for P55859 (Bos taurus) Explore P55859  Go to UniProtKB:  P55859

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.248 (Depositor) 
• R-Value Work:  0.222 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.72	α = 90
b = 92.72	β = 90
c = 92.72	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-30 
Deposition Author(s): Pugmire, M.J., Mao, C., Ealick, S.E.

Revision History  

• Version 1.0: 1999-03-30
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Other