4IWX

Rimk structure at 2.85A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.854 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


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:  

  • 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-gr ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S6 modification protein
A
320Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rimK
EC: 6.3.2.-
Find proteins for P0C0U4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C0U4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GLU
Query on GLU

Download SDF File 
Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.854 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 129.802α = 90.00
b = 129.802β = 90.00
c = 171.239γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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