4LDN

Crystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri ES114 (Target NYSGRC-029521)

• PDB DOI: https://doi.org/10.2210/pdb4LDN/pdb

• Classification: TRANSFERASE
• Organism(s): Aliivibrio fischeri ES114
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-24 Released: 2013-07-03 
• Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.187 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Crystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri ES114 (Target NYSGRC-029521)

Sampathkumar, P., Ahmed, M., Attonito, J., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Eromenok, G., Fiser, A., Glenn, A.S., Hammonds, J., Himmel, D.M., Hillerich, B., Khafizov, K., Lafleur, J., Love, J.D., Stead, M., Seidel, R., Toro, R., Morisco, L.L., Sojitra, S.S., Wasserman, S.R., Suarez, J., Schramm, V.L., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 30.24 kDa 
• Atom Count: 2,161 
• Modelled Residue Count: 244 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase DeoD-type	A	261	Aliivibrio fischeri ES114	Mutation(s): 0  Gene Names: deoD3, VF_A0968 EC: 2.4.2.1
UniProt
Find proteins for Q5DYV8 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5DYV8  Go to UniProtKB:  Q5DYV8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.48 Å
• R-Value Free: 0.187 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.115	α = 90
b = 163.115	β = 90
c = 45.339	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
Aimless	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description