5XGF | pdb_00005xgf

The fatty acid-responsive FadR repressor of Vibrio alginolyticus

• PDB DOI: https://doi.org/10.2210/pdb5XGF/pdb
• Entry: 5XGF supersedes: 5DV1

• Classification: TRANSCRIPTION
• Organism(s): Vibrio diabolicus E0666
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-13 Released: 2017-05-31 
• Deposition Author(s): Lin, Y., Li, D.F., Feng, Y.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Snapshort of Vibrio FadR-ligand complex structure reveals a new mechanism for bacterial fatty acid sensing

Feng, Y.J., Lin, Y., Li, D.F., Zhang, H.M., Gao, R.S., Bi, L.J., Wang, S.H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.46 kDa 
• Atom Count: 2,312 
• Modeled Residue Count: 271 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid metabolism regulator protein	A	300	Vibrio diabolicus E0666	Mutation(s): 0
UniProt
Find proteins for A0A0H0Y8X2 (Vibrio alginolyticus) Explore A0A0H0Y8X2  Go to UniProtKB:  A0A0H0Y8X2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76	α = 90
b = 76	β = 90
c = 144.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Lin, Y., Li, D.F., Feng, Y.J.
• This entry supersedes: 5DV1

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description