9FKU | pdb_00009fku

Crystal Structure of AimR from Katmira phage

• PDB DOI: https://doi.org/10.2210/pdb9FKU/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-06-04 Released: 2025-06-18 
• Deposition Author(s): Gallego del Sol, F., Marina, A.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.212 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of AimR from Katmira phage

Gallego del Sol, F., Marina, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 92.17 kDa 
• Atom Count: 6,875 
• Modeled Residue Count: 784 
• Deposited Residue Count: 784 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arbitrium receptor	A, B	386	Bacillus subtilis	Mutation(s): 0
UniProt
Find proteins for O31927 (Bacillus subtilis (strain 168)) Explore O31927  Go to UniProtKB:  O31927

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-VAL-VAL-ARG-GLY-ALA	C, D	6	Bacillus subtilis	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth A], H [auth B], I [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	F [auth A], G [auth A], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.212 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.765	α = 90
b = 203.582	β = 90
c = 143.069	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Gallego del Sol, F., Marina, A.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release