4LDN

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase DeoD-type
A
261Aliivibrio fischeri (strain ATCC 700601 / ES114)Mutation(s): 0 
Gene Names: deoD3
EC: 2.4.2.1
Find proteins for Q5DYV8 (Aliivibrio fischeri (strain ATCC 700601 / ES114))
Go to UniProtKB:  Q5DYV8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.162 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 163.115α = 90.00
b = 163.115β = 90.00
c = 45.339γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SHELXphasing
SHELXEmodel building
Aimlessdata scaling
XDSdata reduction
REFMACrefinement
CBASSdata collection
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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