2F5N | pdb_00002f5n

MutM crosslinked to undamaged DNA sampling A:T base pair IC1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history. 

Literature

Structure of a DNA glycosylase searching for lesions.

Banerjee, A., Santos, W.L., Verdine, G.L.

(2006) Science 311: 1153-1157

  • DOI: https://doi.org/10.1126/science.1120288
  • Primary Citation Related Structures: 
    2F5N, 2F5O, 2F5P, 2F5Q, 2F5S

  • PubMed Abstract: 

    DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.

    • Organizational Affiliation: 
    • Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

Macromolecule Content 

  • Total Structure Weight: 40.76 kDa 
  • Atom Count: 2,630 
  • Modeled Residue Count: 279 
  • Deposited Residue Count: 306 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
formamidopyrimidine-DNA glycosidaseC [auth A]274Geobacillus stearothermophilusMutation(s): 1 
EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt
Find proteins for P84131 (Geobacillus stearothermophilus)
Explore P84131 
Go to UniProtKB:  P84131
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84131
Sequence Annotations
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'A [auth B]16N/A
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*TP*GP*C*GP*TP*CP*CP*AP*GP*GP*TP*CP*TP*AP*CP*C)-3'B [auth C]16N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.379α = 90
b = 92.947β = 90
c = 105.195γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2015-07-08
    Changes: Structure summary
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description