5UK7 | pdb_00005uk7

Escherichia coli Hfq bound to dsDNA

• PDB DOI: https://doi.org/10.2210/pdb5UK7/pdb
• NAKB: 5UK7

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-20 Released: 2018-05-09 
• Deposition Author(s): Orans, J., Kovach, A.R., Brennan, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Escherichia coli Hfq DNA complex reveals multifunctional nucleic acid binding site

Orans, J., Kovach, A.R., Hoff, K.E., Brennan, R.G.

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.94 kDa 
• Atom Count: 8,044 
• Modeled Residue Count: 872 
• Deposited Residue Count: 896 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein Hfq	A, B, C, D, E, F, G, H, I, J, K, L	68	Escherichia coli	Mutation(s): 0  Gene Names: hfq, A6I92_23385, AWG90_11910, HMPREF3040_03060
UniProt
Find proteins for P0A6X3 (Escherichia coli (strain K12)) Explore P0A6X3  Go to UniProtKB:  P0A6X3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*GP*CP*AP*AP*AP*AP*AP*A)-3')	M [auth N], P [auth Z]	20	Escherichia coli

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*GP*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*CP*G)-3')	N [auth M], O [auth Y]	20	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AA [auth K], BA [auth L], Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.749	α = 105.93
b = 65.795	β = 92.28
c = 81.996	γ = 119.92

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing
HKL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Orans, J., Kovach, A.R., Brennan, R.G.

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description