4IWX

Rimk structure at 2.85A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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This is version 1.2 of the entry. See complete history


Literature

Structure and function of Escherichia coli RimK, an ATP-grasp fold, l-glutamyl ligase enzyme.

Zhao, G.Jin, Z.Wang, Y.Allewell, N.M.Tuchman, M.Shi, D.

(2013) Proteins 81: 1847-1854

  • DOI: 10.1002/prot.24311
  • Primary Citation of Related Structures:  
    4IWX, 4IWY

  • PubMed Abstract: 
  • We report herein the crystal structure of Escherichia coli RimK at a resolution of 2.85 Å, an enzyme that catalyzes the post-translational addition of up to 15 C-terminal glutamate residues to ribosomal protein S6. The structure belongs to the ATP-grasp superfamily and is organized as a tetramer, consistent with gel filtration analysis ...

    We report herein the crystal structure of Escherichia coli RimK at a resolution of 2.85 Å, an enzyme that catalyzes the post-translational addition of up to 15 C-terminal glutamate residues to ribosomal protein S6. The structure belongs to the ATP-grasp superfamily and is organized as a tetramer, consistent with gel filtration analysis. Each subunit consists of three distinct structural domains and the active site is located in the cleft between these domains. The catalytic reaction appears to occur at the junction between the three domains as ATP binds between the B and C domains, and other substrates bind nearby.


    Organizational Affiliation

    Department of Integrative Systems Biology, Center for Genetic Medicine Research, Children's National Medical Center, The George Washington University, Washington, DC, 20010.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S6 modification proteinA320Escherichia coli K-12Mutation(s): 0 
Gene Names: b0852JW0836rimK
EC: 6.3.2
UniProt
Find proteins for P0C0U4 (Escherichia coli (strain K12))
Explore P0C0U4 
Go to UniProtKB:  P0C0U4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.802α = 90
b = 129.802β = 90
c = 171.239γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
DENZOdata reduction
SHELXSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description