2gx2

Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa

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 monomer	Monomer	Protein 1	MAGNESIUM ION × 6 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 6 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 8 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 8 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 7 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 7 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 5 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 3 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 4 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 4 water × 1	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 21–241； UniProt 2–224 Author chain B； PDBConstruct 21–241； UniProt 2–224 Author chain C； PDBConstruct 21–241； UniProt 2–224 Author chain D； PDBConstruct 21–241； UniProt 2–224 Author chain E； PDBConstruct 21–241； UniProt 2–224 Author chain F； PDBConstruct 21–241； UniProt 2–224 Author chain G； PDBConstruct 21–241； UniProt 2–224 Author chain H； PDBConstruct 21–241； UniProt 2–224 Author chain I； PDBConstruct 21–241； UniProt 2–224 Author chain J； PDBConstruct 21–241； UniProt 2–224 Author chain K； PDBConstruct 21–241； UniProt 2–224 Author chain L； PDBConstruct 21–241； UniProt 2–224

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	2gx2
Deposition date deposition_date	2006-05-08
Structure title title	Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa
Keywords keywords	photoswiching, fluorescence protein, LUMINESCENT PROTEIN; LUMINESCENT 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.

2gx2__assembly_9__model_1

Assembly 9 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2gx2__assembly_9__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gx2__assembly_9__model_1 | P(r) · Pending

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

Rg（Guinier）	17.79 Å
Rg (electron density)	16.64 Å
Total Rg	17.73 Å
Atom count	1766
Residues	217
Excluded volume	31273 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gx2__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2gx2__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2gx2__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2gx2__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2gx2__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2gx2__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2gx2__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2gx2__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2gx2__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`2gx2__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`2gx2__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`2gx2__assembly_12__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	fluorescent protein Dronpa
Molecular weight formula_weight	27597.2 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	23035

MRGSHHHHHHGSLVPRGSMVSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFXNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSELPRQAK

Source Source

Source organism organism	Echinophyllia sp. SC22
Common name common_name	coral
NCBI taxonomy ID ncbi_taxonomy_id	301887
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	62

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2032

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2gx2a_
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	d2gx2b_
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	d2gx2c_
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	d2gx2d_
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	d2gx2e_
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	d2gx2f_
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	d2gx2g_
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	d2gx2h_
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	d2gx2i_
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	d2gx2j_
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	d2gx2k_
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	d2gx2l_
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

CATH v4.4 (12 domains)

Domain ID domain_id	2gx2A00
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	2gx2B00
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	2gx2C00
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	2gx2D00
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	2gx2E00
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	2gx2F00
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	2gx2G00
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	2gx2H00
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	2gx2I00
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	2gx2J00
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	2gx2K00
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	2gx2L00
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	73.091 Å
Unit-cell length b length_b	106.160 Å
Unit-cell length c length_c	110.070 Å
Unit-cell angle α angle_alpha	61.17 °
Unit-cell angle β angle_beta	70.85 °
Unit-cell angle γ angle_gamma	86.21 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2090

Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa

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

2gx2__assembly_9__model_1

2gx2__assembly_9__model_1 | I(q)

2gx2__assembly_9__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa

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

2gx2__assembly_9__model_1

2gx2__assembly_9__model_1 | I(q)

2gx2__assembly_9__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)