1SYY | pdb_00001syy

Crystal structure of the R2 subunit of ribonucleotide reductase from Chlamydia trachomatis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1SYY

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

Literature

The radical site in chlamydial ribonucleotide reductase defines a new R2 subclass.

Hogbom, M., Stenmark, P., Voevodskaya, N., McClarty, G., Graslund, A., Nordlund, P.

(2004) Science 305: 245-248

  • DOI: https://doi.org/10.1126/science.1098419
  • Primary Citation Related Structures: 
    1SYY

  • PubMed Abstract: 

    Ribonucleotide reductase (RNR) synthesizes the deoxyribonucleotides for DNA synthesis. The R2 protein of normal class I ribonucleotide reductases contains a diiron site that produces a stable tyrosyl free radical, essential for enzymatic activity. Structural and electron paramagnetic resonance studies of R2 from Chlamydia trachomatis reveal a protein lacking a tyrosyl radical site. Instead, the protein yields an iron-coupled radical upon reconstitution. The coordinating structure of the diiron site is similar to that of diiron oxidases/monoxygenases and supports a role for this radical in the RNR mechanism. The specific ligand pattern in the C. trachomatis R2 metal site characterizes a new group of R2 proteins that so far has been found in eight organisms, three of which are human pathogens.

    • Organizational Affiliation: 
    • Department of Biochemistry and Biophysics, Stockholm University, Roslagstullsbacken 15, Albanova University Center, SE-10691 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 40.88 kDa 
  • Atom Count: 3,011 
  • Modeled Residue Count: 317 
  • Deposited Residue Count: 346 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase beta chain346Chlamydia trachomatisMutation(s): 0 
Gene Names: NRDB, CT828
EC: 1.17.4.1
UniProt
Find proteins for O84835 (Chlamydia trachomatis serovar D (strain ATCC VR-885 / DSM 19411 / UW-3/Cx))
Explore O84835 
Go to UniProtKB:  O84835
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO84835
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.738α = 90
b = 62.738β = 90
c = 171.797γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
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: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Advisory, Data collection
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations