5HZS | pdb_00005hzs

Crystal structure of Dronpa-Co2+

PDB DOI: https://doi.org/10.2210/pdb5HZS/pdb

Classification: LUMINESCENT PROTEIN
Organism(s): Echinophyllia sp. SC22
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-02-03 Released: 2017-03-15
Deposition Author(s): Hwang, K.Y., Nam, K.H.
Funding Organization(s): National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.225 (Depositor), 0.232 (DCC)
R-Value Work:
0.166 (Depositor), 0.177 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Literature

Crystal structures of Dronpa complexed with quenchable metal ions provide insight into metal biosensor development

Kim, I.J., Kim, S., Park, J., Eom, I., Kim, S., Kim, J.H., Ha, S.C., Kim, Y.G., Hwang, K.Y., Nam, K.H.

(2016) FEBS Lett 590: 2982-2990

PubMed: 27433793 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12316
Primary Citation Related Structures:
5HZS, 5HZT, 5HZU

PubMed Abstract:
Many fluorescent proteins (FPs) show fluorescence quenching by specific metal ions, which can be applied towards metal biosensor development. In this study, we investigated the significant fluorescence quenching of Dronpa by Co(2+) and Cu(2+) ions. Crystal structures of Co(2+) -, Ni(2+) - and Cu(2+) -bound Dronpa revealed previously unseen, unique, metal-binding sites for fluorescence quenching. These metal ions commonly interact with surface-exposed histidine residues (His194-His210 and His210-His212), and interact indirectly with chromophores. Structural analysis of the Co(2+) - and Cu(2+) - binding sites of Dronpa provides insight into FP-based metal biosensor engineering.

Organizational Affiliation

Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 297.27 kDa
Atom Count: 22,118
Modeled Residue Count: 2,569
Deposited Residue Count: 2,580
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, G, H, I, J, K, L	215	Echinophyllia sp. SC22	Mutation(s): 1 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain FA [auth J] SDF format, chain Z [auth G] SDF format, chain Y [auth G] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain JA [auth L] SDF format, chain IA [auth L] SDF format, chain HA [auth K] SDF format, chain GA [auth K] SDF format, chain EA [auth J] SDF format, chain DA [auth I] SDF format, chain CA [auth I] SDF format, chain AA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain FA [auth J] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain IA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain GA [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain CA [auth I] MOL2 format, chain AA [auth H] mmCIF format, chain BA [auth H] mmCIF format, chain FA [auth J] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain IA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain GA [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain CA [auth I] mmCIF format, chain AA [auth H]	AA [auth H] BA [auth H] CA [auth I] DA [auth I] EA [auth J] AA [auth H], BA [auth H], CA [auth I], DA [auth I], EA [auth J], FA [auth J], GA [auth K], HA [auth K], IA [auth L], JA [auth L], M [auth A], N [auth A], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth D], T [auth D], U [auth E], V [auth E], W [auth F], X [auth F], Y [auth G], Z [auth G]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYS Query on GYS	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₅		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.225 (Depositor), 0.232 (DCC)
R-Value Work: 0.166 (Depositor), 0.177 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.33	α = 115.79
b = 105.479	β = 109.51
c = 109.776	γ = 93.95

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

Hwang, K.Y.

Nam, K.H.

Funding Organization	Location	Grant Number
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)	Korea, Republic Of	NRF-2014R1A1A2059440
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)	Korea, Republic Of	NRF-2014R1212513

Revision History (Full details and data files)

Version 1.0: 2017-03-15
Type: Initial release
Version 1.1: 2018-11-28
Changes: Data collection, Database references
Version 1.2: 2019-11-20
Changes: Derived calculations
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2024-11-13
Changes: Structure summary
Version 3.0: 2026-03-18
Changes: Polymer sequence