5ZK6 | pdb_00005zk6

Crystal structure of RimK complexed with RpsF

• PDB DOI: https://doi.org/10.2210/pdb5ZK6/pdb

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


• Deposited: 2018-03-23 Released: 2019-03-27 
• Deposition Author(s): Arimura, Y., Kono, T., Kino, K., Kurumizaka, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Molecular dynamics prediction of substrate recognition by poly-alpha-L-glutamate synthetase

Ohnuki, J., Arimura, Y., Kono, T., Kino, K., Kurumizaka, H., Takano, M.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.56 kDa 
• Atom Count: 2,234 
• Modeled Residue Count: 291 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6--L-glutamate ligase	A	306	Escherichia coli K-12	Mutation(s): 0  Gene Names: rimK EC: 6.3.2
UniProt
Find proteins for P0C0U4 (Escherichia coli (strain K12)) Explore P0C0U4  Go to UniProtKB:  P0C0U4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.272	α = 90
b = 131.272	β = 90
c = 168.571	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Arimura, Y., Kono, T., Kino, K., Kurumizaka, H.

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary