5DV5 | pdb_00005dv5

The fatty acid-responsive FadR repressor of Vibrio alginolyticus complex with Palmitoyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb5DV5/pdb

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


• Deposited: 2015-09-21 Released: 2016-10-05 
• Deposition Author(s): Lin, Y., Li, D.F., Feng, Y.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (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)

Macromolecule Content 

• Total Structure Weight: 72.83 kDa 
• Atom Count: 4,675 
• Modeled Residue Count: 534 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GntR family transcriptional regulator	A, B	300	Vibrio alginolyticus	Mutation(s): 0  Gene Names: AAW52_18775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PKZ	C [auth A], D [auth A], E [auth B], F [auth B]	Palmitoyl-CoA C37 H66 N7 O17 P3 S MNBKLUUYKPBKDU-BBECNAHFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.78	α = 90
b = 88.48	β = 93.13
c = 61.65	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: 2016-10-05 
Deposition Author(s): Lin, Y., Li, D.F., Feng, Y.J.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description