6nqr

Crystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2)- Y63(3-NO2Y)

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fluorescent protein Dronpa

Echinophyllia sp. SC22

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5TLG6_9CNID
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 31–249； UniProt 3–223 Author chain B； PDBConstruct 31–249； UniProt 3–223 Author chain C； PDBConstruct 31–249； UniProt 3–223 Author chain D； PDBConstruct 31–249； UniProt 3–223 Author chain E； PDBConstruct 31–249； UniProt 3–223 Author chain F； PDBConstruct 31–249； UniProt 3–223 Author chain G； PDBConstruct 31–249； UniProt 3–223 Author chain H； PDBConstruct 31–249； UniProt 3–223

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nqr
Deposition date deposition_date	2019-01-21
Structure title title	Crystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2)- Y63(3-NO2Y)
Keywords keywords	Dronpa2, FLUORESCENT PROTEIN; FLUORESCENT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6nqr__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6nqr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nqr__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.42 Å
Rg (electron density)	27.59 Å
Total Rg	28.59 Å
Atom count	6941
Residues	868
Excluded volume	122530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nqr__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nqr__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (1)

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6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d6nqra1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.0 — automated matches

Domain ID domain_id	d6nqra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nqrb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.0 — automated matches

Domain ID domain_id	d6nqrc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.0 — automated matches

Domain ID domain_id	d6nqrc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nqrd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.0 — automated matches

Domain ID domain_id	d6nqre1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.0 — automated matches

Domain ID domain_id	d6nqre2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nqrf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.0 — automated matches

Domain ID domain_id	d6nqrg1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.0 — automated matches

Domain ID domain_id	d6nqrg2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nqrg3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nqrh1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.22 — GFP-like
Superfamily Superfamily superfamily	d.22.1 — GFP-like
Family Family family	d.22.1.0 — automated matches

Domain ID domain_id	d6nqrh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (5 domains)

Domain ID domain_id	6nqrA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6nqrB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6nqrF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6nqrG00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	6nqrH00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

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Unit-cell length a length_a	71.610 Å
Unit-cell length b length_b	79.430 Å
Unit-cell length c length_c	85.930 Å
Unit-cell angle α angle_alpha	89.96 °
Unit-cell angle β angle_beta	92.53 °
Unit-cell angle γ angle_gamma	94.76 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	37.510 Å
R factor r_factor	0.2200
R_work r_work	0.2160
R_free r_free	0.2830

Description description	Fluorescent protein Dronpa
Molecular weight formula_weight	29006.6 kDa
Mutation mutation	M159T, E218G
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	13844

Crystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2)- Y63(3-NO2Y)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Fluorescent protein Dronpa

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6nqr__assembly_2__model_1

6nqr__assembly_2__model_1 | I(q)

6nqr__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (14 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Source organism organism	Echinophyllia sp. SC22
NCBI taxonomy ID ncbi_taxonomy_id	301887
Host organism host_organism	Escherichia coli BL21(DE3)

Crystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2)- Y63(3-NO2Y)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Fluorescent protein Dronpa

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6nqr__assembly_2__model_1

6nqr__assembly_2__model_1 | I(q)

6nqr__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (14 domains)

CATH v4.4 (5 domains)

7. Citations (1)