1E3P

tungstate derivative of Streptomyces antibioticus PNPase/GPSI enzyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

A Duplicated Fold is the Structural Basis for Polynucleotide Phosphorylase Catalytic Activity, Processivity, and Regulation

Symmons, M.F., Jones, G.H., Luisi, B.F.

(2000) Structure 8: 1215

  • DOI: https://doi.org/10.1016/s0969-2126(00)00521-9
  • Primary Citation of Related Structures:  
    1E3H, 1E3P

  • PubMed Abstract: 

    Polynucleotide phosphorylase (PNPase) is a polyribonucleotide nucleotidyl transferase (E.C.2.7.7.8) that degrades mRNA in prokaryotes. Streptomyces antibioticus PNPase also assays as a guanosine 3'-diphosphate 5'-triphosphate (pppGpp) synthetase (E.C.2.7.6.5). It may function to coordinate changes in mRNA lifetimes with pppGpp levels during the Streptomyces lifecycle.

    • Organizational Affiliation: 

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom. mfs@mole.bio.cam.ac.uk


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyribonucleotide nucleotidyltransferase757Streptomyces antibioticusMutation(s): 0 
Gene Names: pnp, AFM16_28085
EC: 2.7.7.8
UniProt
Find proteins for Q53597 (Streptomyces antibioticus)
Explore Q53597 
Go to UniProtKB:  Q53597
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53597
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WO4
Query on WO4
Download Ideal Coordinates CCD File 
L [auth A]TUNGSTATE(VI)ION
O4 W
PBYZMCDFOULPGH-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.83α = 90
b = 130.83β = 90
c = 328.732γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-06
    Changes: Advisory, Data collection, Database references, Other, Source and taxonomy, Structure summary
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description