1UZR | pdb_00001uzr

Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 subunit from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.202 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Biologically Active Form of Class Ib Ribonucleotide Reductase Small Subunit from Mycobacterium Tuberculosis

Uppsten, M.Davis, J.Rubin, H.Uhlin, U.

(2004) FEBS Lett 569: 117

  • DOI: https://doi.org/10.1016/j.febslet.2004.05.059
  • Primary Citation Related Structures: 
    1UZR

  • PubMed Abstract: 

    Two nrdF genes of Mycobacterium tuberculosis code for different R2 subunits of the class Ib ribonucleotide reductase (RNR). The proteins are denoted R2F-1 and R2F-2 having 71% sequence identity. The R2F-2 subunit forms the biologically active RNR complex with the catalytic R1E-subunit. We present the structure of the reduced R2F-2 subunit to 2.2 A resolution. Comparison of the R2F-2 structure with a model of R2F-1 suggests that the important differences are located at the C-terminus. We found that within class Ib, the E-helix close to the iron diiron centre has two preferred conformations, which cannot be explained by the redox-state of the diiron centre. In the R2F-2 structure, we also could see a mobility of alphaE in between the two conformations.


  • Organizational Affiliation
    • Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center, P.O. Box 590, SE-751 24 Uppsala, Sweden.

Macromolecule Content 

  • Total Structure Weight: 102.71 kDa 
  • Atom Count: 7,359 
  • Modeled Residue Count: 853 
  • Deposited Residue Count: 888 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
A, B, C
296Mycobacterium tuberculosisMutation(s): 0 
EC: 1.17.4.1
UniProt
Find proteins for P9WH71 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH71 
Go to UniProtKB:  P9WH71
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WH71
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on CIT



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
N [auth C]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
O [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
H [auth B]
I [auth B]
L [auth C]
D [auth A],
E [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.492α = 90
b = 161.492β = 90
c = 115.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-08
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description