3IBP

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

• PDB DOI:  https://doi.org/10.2210/pdb3IBP/pdb

• Classification: CELL CYCLE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-16 Released: 2010-01-26 
• Deposition Author(s): Li, Y., Schoeffler, A.J., Berger, J.M., Oakley, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.243 
• R-Value Observed: 0.247 

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 Biol 395: 11-19

• PubMed: 19853611 
• DOI: https://doi.org/10.1016/j.jmb.2009.10.040
• Primary Citation of 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.

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Organizational Affiliation: 

Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome partition protein mukB	A	302	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0924, JW0907, mukB
UniProt
Find proteins for P22523 (Escherichia coli (strain K12)) Explore P22523  Go to UniProtKB:  P22523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NH4	B [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.243 
• R-Value Observed: 0.247 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.27	α = 90
b = 56.27	β = 90
c = 342.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Li, Y., Schoeffler, A.J., Berger, J.M., Oakley, M.G.

Revision History  

• 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