5DJT

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.171
R-Value Work: 0.146
R-Value Observed: 0.147

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O49004
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered protein, Zdk2 affibody	B	61	Staphylococcus aureus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.171
R-Value Work: 0.146
R-Value Observed: 0.147
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Revision History (Full details and data files)

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