4NS1

Crystal structure of purine nucleoside phosphorylase from Porphyromonas gingivalis ATCC 33277, NYSGRC Target 30972


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of purine nucleoside phosphorylase from Porphyromonas gingivalis ATCC 33277, NYSGRC Target 30972.

Malashkevich, V.N.Bhosle, R.Toro, R.Hillerich, B.Gizzi, A.Garforth, S.Kar, A.Chan, M.K.Lafluer, J.Patel, H.Matikainen, B.Chamala, S.Lim, S.Celikgil, A.Villegas, G.Evans, B.Love, J.Fiser, A.Seidel, R.Bonanno, J.B.Almo, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
A, B, C, D
295Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)Mutation(s): 0 
EC: 2.4.2.1
Find proteins for B2RKN6 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Go to UniProtKB:  B2RKN6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DA
Query on DA

Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.171 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 218.904α = 90.00
b = 218.904β = 90.00
c = 218.904γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
REFMACrefinement
CBASSdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release