4IWX

Rimk structure at 2.85A

• PDB DOI: https://doi.org/10.2210/pdb4IWX/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-24 Released: 2013-05-08 
• Deposition Author(s): Shi, D., Zhao, G., Jin, Z., Allewell, N.M., Tuchman, M.

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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 

Starting Model: experimental

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

• PubMed: 23609986 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 35.71 kDa 
• Atom Count: 2,316 
• Modelled Residue Count: 294 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6 modification protein	A	320	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0852, JW0836, rimK EC: 6.3.2
UniProt
Find proteins for P0C0U4 (Escherichia coli (strain K12)) Explore P0C0U4  Go to UniProtKB:  P0C0U4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GLU	C [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 129.802	α = 90
b = 129.802	β = 90
c = 171.239	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Shi, D., Zhao, G., Jin, Z., Allewell, N.M., Tuchman, M.

Revision History  

• 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
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description