Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 36.21 kDa 
• Atom Count: 2960 
• Modelled Residue Count: 318 
• Deposited Residue Count: 320 
• Unique protein chains: 1

2FA1

Crystal structure of PhnF C-terminal domain

• PDB DOI: 10.2210/pdb2FA1/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-12-06 Released: 2006-01-10 
• Deposition Author(s): Lunin, V.V., Nocek, B.P., Gorelik, M., Skarina, T., Edwards, A.M., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.241 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

Structural characterization of GntR/HutC family signaling domain.

Gorelik, M., Lunin, V.V., Skarina, T., Savchenko, A.

(2006) Protein Sci 15: 1-6

• PubMed: 16672238 
• DOI: 10.1110/ps.062146906
• Primary Citation of Related Structures:  
  2FA1


• PubMed Abstract: 
  

The crystal structure of Escherichia coli PhnF C-terminal domain (C-PhnF) was solved at 1.7 A resolution by the single wavelength anomalous dispersion (SAD) method. The PhnF protein belongs to the HutC subfamily of the large GntR transcriptional regulator family. Members of this family share similar N-terminal DNA-binding domains, but are divided into four subfamilies according to their heterogenic C-terminal domains, which are involved in effector binding and oligomerization. The C-PhnF structure provides for the first time the scaffold of this domain for the HutC subfamily, which covers about 31% of GntR-like regulators. The structure represents a mixture of alpha-helices and beta-strands, with a six-stranded antiparallel beta-sheet at the core. C-PhnF monomers form a dimer by establishing interdomain eight-strand beta-sheets that include core antiparallel and N-terminal two-strand parallel beta-sheets from each monomer. C-PhnF shares strong structural similarity with the chorismate lyase fold, which features a buried active site locked behind two helix-turn-helix loops. The structural comparison of the C-PhnF and UbiC proteins allows us to propose that a similar site in the PhnF structure is adapted for effector binding.

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Organizational Affiliation: 

Ontario Center for Structural Proteomics, University Health Network, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator phnF	A, B	160	Escherichia coli	Mutation(s): 0  Gene Names: phnF
UniProt
Find proteins for P16684 (Escherichia coli (strain K12)) Explore P16684  Go to UniProtKB:  P16684

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDF	C [auth B]	beta-D-fructopyranose C6 H12 O6 LKDRXBCSQODPBY-ARQDHWQXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.241 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.765	α = 90
b = 51.572	β = 103.64
c = 63.961	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-06 
• Released Date: 2006-01-10 
Deposition Author(s): Lunin, V.V., Nocek, B.P., Gorelik, M., Skarina, T., Edwards, A.M., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-01-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-10-05
  Changes: Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary