3N3B | pdb_00003n3b

Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.275 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.234 (Depositor) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structural basis for activation of class Ib ribonucleotide reductase.

Boal, A.K.Cotruvo, J.A.Stubbe, J.Rosenzweig, A.C.

(2010) Science 329: 1526-1530

  • DOI: https://doi.org/10.1126/science.1190187
  • Primary Citation Related Structures: 
    3N37, 3N38, 3N39, 3N3A, 3N3B

  • PubMed Abstract: 

    The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)2-tyrosyl radical (Y•) or a Fe(III)2-Y• cofactor in the NrdF subunit. Whereas Fe(III)2-Y• can self-assemble from Fe(II)2-NrdF and O2, activation of Mn(II)2-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O2. The crystal structures reported here of E. coli Mn(II)2-NrdF and Fe(II)2-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)2-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)2 active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)2-Y• cofactor assembly.


  • Organizational Affiliation
    • Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208, USA.

Macromolecule Content 

  • Total Structure Weight: 108.58 kDa 
  • Atom Count: 6,885 
  • Modeled Residue Count: 826 
  • Deposited Residue Count: 944 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 2 subunit betaA [auth B],
C [auth A]
319Escherichia coli K-12Mutation(s): 0 
Gene Names: b2676JW2651nrdFygaD
EC: 1.17.4.1
UniProt
Find proteins for P37146 (Escherichia coli (strain K12))
Explore P37146 
Go to UniProtKB:  P37146
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37146
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein nrdIB [auth C],
D
153Escherichia coli K-12Mutation(s): 0 
Gene Names: nrdIygaOb2674JW2649
UniProt
Find proteins for P0A772 (Escherichia coli (strain K12))
Explore P0A772 
Go to UniProtKB:  P0A772
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A772
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN



Download:Ideal Coordinates CCD File
H [auth C],
L [auth D]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
E [auth B],
F [auth B],
I [auth A],
J [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
PEO

Query on PEO



Download:Ideal Coordinates CCD File
G [auth B],
K [auth A]
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.275 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.234 (Depositor) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.723α = 90
b = 91.348β = 90
c = 144.114γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description