4UC0

Crystal Structure Of a purine nucleoside phosphorylase (PSI-NYSGRC-029736) from Agrobacterium vitis

• PDB DOI: https://doi.org/10.2210/pdb4UC0/pdb

• Classification: TRANSFERASE
• Organism(s): Agrobacterium vitis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-13 Released: 2014-10-08 
• Deposition Author(s): Cameron, S.A., Sampathkumar, P., Ramagopal, U.A., Attonito, J., Ahmed, M., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Glenn, A.S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Wasserman, S.R., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.224 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Literature

Crystal Structure Of a purine nucleoside phosphorylase (PSI-NYSGRC-029736) from Agrobacterium vitis

Cameron, S.A., Sampathkumar, P., Ramagopal, U.A., Attonito, J., Ahmed, M., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Glenn, A.S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Wasserman, S.R., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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: 31.46 kDa 
• Atom Count: 1,834 
• Modelled Residue Count: 247 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A	291	Agrobacterium vitis	Mutation(s): 0  Gene Names: Avi_0263 EC: 2.4.2.1
UniProt
Find proteins for B9JYS2 (Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4)) Explore B9JYS2  Go to UniProtKB:  B9JYS2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HPA	B [auth A]	HYPOXANTHINE C5 H4 N4 O FDGQSTZJBFJUBT-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.224 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.881	α = 90
b = 97.881	β = 90
c = 46.356	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data reduction
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Cameron, S.A., Sampathkumar, P., Ramagopal, U.A., Attonito, J., Ahmed, M., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Glenn, A.S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Wasserman, S.R., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence, Data collection, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Refinement description