3W1O | pdb_00003w1o

Neisseria DNA mimic protein DMP12

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein

Wang, H.C., Wu, M.L., Ko, T.P., Wang, A.H.

(2013) Nucleic Acids Res 41: 5127-5138

  • DOI: https://doi.org/10.1093/nar/gkt201
  • Primary Citation Related Structures: 
    3W1O

  • PubMed Abstract: 

    DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

    • Organizational Affiliation: 
    • Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 28.19 kDa 
  • Atom Count: 2,231 
  • Modeled Residue Count: 230 
  • Deposited Residue Count: 238 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA mimic protein DMP12
A, B
119Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: NMB2123
UniProt
Find proteins for Q9JXC6 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58))
Explore Q9JXC6 
Go to UniProtKB:  Q9JXC6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JXC6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.519α = 90
b = 112.519β = 90
c = 57.128γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SHELXCDphasing
SHELXEmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description, Structure summary
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations