6EBZ

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae in Activated Form with Thiocyanate Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.

Blaesi, E.J.Palowitch, G.M.Hu, K.Kim, A.J.Rose, H.R.Alapati, R.Lougee, M.G.Kim, H.J.Taguchi, A.T.Tan, K.O.Laremore, T.N.Griffin, R.G.Krebs, C.Matthews, M.L.Silakov, A.Bollinger Jr., J.M.Allen, B.D.Boal, A.K.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 10022-10027


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleoside-diphosphate reductase, beta subunit
A, B, C, D
355Aerococcus urinae (strain ACS-120-V-Col10a)Mutation(s): 0 
EC: 1.17.4.1
Find proteins for F2I8X9 (Aerococcus urinae (strain ACS-120-V-Col10a))
Go to UniProtKB:  F2I8X9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
B, C
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DAH
Query on DAH
A, B, C, D
L-PEPTIDE LINKINGC9 H11 N O4PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.041α = 90.00
b = 108.973β = 90.14
c = 84.031γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM119707

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Database references
  • Version 1.2: 2018-10-17
    Type: Data collection, Database references
  • Version 1.3: 2019-01-30
    Type: Data collection, Structure summary