6CGN

X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit dAMP-bound (pH 7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An endogenous dAMP ligand inBacillus subtilisclass Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP.

Parker, M.J.Maggiolo, A.O.Thomas, W.C.Kim, A.Meisburger, S.P.Ando, N.Boal, A.K.Stubbe, J.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E4594-E4603


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleoside-diphosphate reductase
A
700Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: nrdE (nrdA)
EC: 1.17.4.1
Find proteins for P50620 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P50620
Small Molecules
Ligands 3 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
DA
Query on DA

Download SDF File 
Download CCD File 
A
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.266α = 90.00
b = 72.266β = 90.00
c = 292.637γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-05-23
    Type: Data collection, Database references