4EMQ | pdb_00004emq

Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4

PDB DOI: https://doi.org/10.2210/pdb4EMQ/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Echinophyllia sp. SC22
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-04-12 Released: 2012-11-21
Deposition Author(s): Ngan, N.B., Van Hecke, K., Van Meervelt, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.232 (Depositor), 0.227 (DCC)
R-Value Work:
0.183 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa.

Nguyen Bich, N., Moeyaert, B., Van Hecke, K., Dedecker, P., Mizuno, H., Hofkens, J., Van Meervelt, L.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1653-1659

PubMed: 23151630 Search on PubMed
DOI: https://doi.org/10.1107/S0907444912039686
Primary Citation Related Structures:
4EMQ

PubMed Abstract:
The crystal structure of the on-state of PDM1-4, a single-mutation variant of the photochromic fluorescent protein Dronpa, is reported at 1.95 Å resolution. PDM1-4 is a Dronpa variant that possesses a slower off-switching rate than Dronpa and thus can effectively increase the image resolution in subdiffraction optical microscopy, although the precise molecular basis for this change has not been elucidated. This work shows that the Lys145Asn mutation in PDM1-4 stabilizes the interface available for dimerization, facilitating oligomerization of the protein. No significant changes were observed in the chromophore environment of PDM1-4 compared with Dronpa, and the ensemble absorption and emission properties of PDM1-4 were highly similar to those of Dronpa. It is proposed that the slower off-switching rate in PDM1-4 is caused by a decrease in the potential flexibility of certain β-strands caused by oligomerization along the AC interface.

Organizational Affiliation

Biomolecular Architecture, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven (Heverlee), Belgium.

Macromolecule Content

Total Structure Weight: 177.8 kDa
Atom Count: 11,412
Modeled Residue Count: 1,286
Deposited Residue Count: 1,530
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorescent protein Dronpa	A, B, C, D, E A, B, C, D, E, F	255	Echinophyllia sp. SC22	Mutation(s): 2 Gene Names: Dronpa
UniProt
Find proteins for Q5TLG6 (Echinophyllia sp. SC22) Explore Q5TLG6 Go to UniProtKB: Q5TLG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5TLG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] K [auth C] N [auth D] P [auth E] G [auth A], I [auth B], K [auth C], N [auth D], P [auth E], R [auth F]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B]	J [auth B] L [auth C] M [auth C] O [auth D] Q [auth E] J [auth B], L [auth C], M [auth C], O [auth D], Q [auth E], S [auth F], T [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYC Query on GYC	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₄ S		CYS, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.232 (Depositor), 0.227 (DCC)
R-Value Work: 0.183 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.539	α = 90
b = 103.804	β = 90
c = 177.255	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASES	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-11-21

Deposition Author(s):

Ngan, N.B.

Van Hecke, K.

Van Meervelt, L.

Revision History (Full details and data files)

Version 1.0: 2012-11-21
Type: Initial release
Version 1.1: 2013-01-23
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2024-10-09
Changes: Structure summary