3IBP | pdb_00003ibp

The Crystal Structure of the Dimerization Domain of Escherichia coli Structural Maintenance of Chromosomes Protein MukB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

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

Literature

The crystal structure of the hinge domain of the Escherichia coli structural maintenance of chromosomes protein MukB.

Li, Y., Schoeffler, A.J., Berger, J.M., Oakley, M.G.

(2010) J Mol Biology 395: 11-19

  • DOI: https://doi.org/10.1016/j.jmb.2009.10.040
  • Primary Citation Related Structures: 
    3IBP

  • PubMed Abstract: 

    MukB, a divergent structural maintenance of chromosomes (SMC) protein, is important for chromosomal segregation and condensation in gamma-proteobacteria. MukB and canonical SMC proteins share a characteristic five-domain structure. Globular N- and C-terminal domains interact to form an ATP-binding cassette-like ATPase or "head" domain, which is connected to a smaller dimerization or "hinge" domain by a long, antiparallel coiled coil. In addition to mediating dimerization, this hinge region has been implicated in both conformational flexibility and dynamic protein-DNA interactions. We report here the first crystallographic model of the MukB hinge domain. This model also contains approximately 20% of the coiled-coil domain, including an unusual coiled-coil deviation. These results will facilitate studies to clarify the roles of both the hinge and the coiled-coil domains in MukB function.

    • Organizational Affiliation: 
    • Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.

Macromolecule Content 

  • Total Structure Weight: 34.66 kDa 
  • Atom Count: 2,291 
  • Modeled Residue Count: 283 
  • Deposited Residue Count: 302 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromosome partition protein mukB302Escherichia coli K-12Mutation(s): 0 
Gene Names: b0924, JW0907, mukB
UniProt
Find proteins for P22523 (Escherichia coli (strain K12))
Explore P22523 
Go to UniProtKB:  P22523
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22523
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NH4

Query on NH4


Download:Ideal Coordinates CCD File
B [auth A]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.27α = 90
b = 56.27β = 90
c = 342.6γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary