3AHU | pdb_00003ahu

Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer.

• PDB DOI: https://doi.org/10.2210/pdb3AHU/pdb
• NAKB: 3AHU

• Classification: TRANSLATION/RNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-29 Released: 2011-07-13 
• Deposition Author(s): Baba, S., Someya, T., Kumasaka, T., Kawai, G., Nakamura, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.260 (Depositor), 0.345 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer.

Someya, T., Baba, S., Fujimoto, M., Kumasaka, T., Kawai, G., Nakamura, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.78 kDa 
• Atom Count: 1,786 
• Modeled Residue Count: 204 
• Deposited Residue Count: 240 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein hfq	A, B, C	78	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU17340, hfq, ymaH
UniProt
Find proteins for O31796 (Bacillus subtilis (strain 168)) Explore O31796  Go to UniProtKB:  O31796

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*AP*GP*AP*GP*AP*G)-3'	D [auth X]	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.260 (Depositor), 0.345 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.921	α = 90
b = 92.504	β = 90
c = 114.918	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Baba, S., Someya, T., Kumasaka, T., Kawai, G., Nakamura, K.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description