5DJT | pdb_00005djt

Crystal structure of LOV2 (C450A) domain in complex with Zdk2

• PDB DOI: https://doi.org/10.2210/pdb5DJT/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Avena sativa, Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-02 Released: 2016-07-20 
• Deposition Author(s): Tarnawski, M., Wang, H., Yumerefendi, H., Hahn, K.M., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Models: experimental

Literature

LOVTRAP: an optogenetic system for photoinduced protein dissociation.

Wang, H., Vilela, M., Winkler, A., Tarnawski, M., Schlichting, I., Yumerefendi, H., Kuhlman, B., Liu, R., Danuser, G., Hahn, K.M.

(2016) Nat Methods 13: 755-758

• PubMed: 27427858 
• DOI: https://doi.org/10.1038/nmeth.3926
• Primary Citation of Related Structures:  
  5DJT, 5DJU, 5EFW


• PubMed Abstract: 
  

  LOVTRAP is an optogenetic approach for reversible light-induced protein dissociation using protein A fragments that bind to the LOV domain only in the dark, with tunable kinetics and a >150-fold change in the dissociation constant (Kd). By reversibly sequestering proteins at mitochondria, we precisely modulated the proteins' access to the cell edge, demonstrating a naturally occurring 3-mHz cell-edge oscillation driven by interactions of Vav2, Rac1, and PI3K proteins.

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Organizational Affiliation: 

Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 23.86 kDa 
• Atom Count: 1,960 
• Modeled Residue Count: 203 
• Deposited Residue Count: 206 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPH1-2	A	145	Avena sativa	Mutation(s): 0  Gene Names: NPH1-2 EC: 2.7.11.1
UniProt
Find proteins for O49004 (Avena sativa) Explore O49004  Go to UniProtKB:  O49004

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered protein, Zdk2 affibody	B	61	Staphylococcus aureus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	D [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CU	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.14	α = 90
b = 110.14	β = 90
c = 37.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Tarnawski, M., Wang, H., Yumerefendi, H., Hahn, K.M., Schlichting, I.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references
• Version 1.2: 2016-09-07
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description