SAXSdb — 2ddd

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

photoconvertible fluorescent protein

Favia favus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q53UG8_9CNID
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–225； UniProt 1–227 Author chain B； PDBConstruct 1–225； UniProt 1–227

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	2ddd
Deposition date deposition_date	2006-01-27
Structure title title	Unique behavior of a histidine responsible for an engineered green-to-red photoconversion process
Keywords keywords	photoconversion, green state, 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.

2ddd__assembly_1__model_1

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

Download this curve (.dat)

2ddd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ddd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.04 Å
Rg (electron density)	23.37 Å
Total Rg	24.31 Å
Atom count	3609
Residues	447
Excluded volume	64239 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ddd__assembly_1__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	photoconvertible fluorescent protein
Molecular weight formula_weight	25705.3 kDa
Mutation mutation	M1V, L12V, E70K, P144S, Q197L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4209

VSVITSEMKIEVRMEGAVNGHKFVITGKGSGQPFEGIQNVDLTVIEGGPLPFAFDILTTAFXNRVFVKYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVNEIRFDGVNFPANGPVMQRKTVKWESSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHLMEITSHDKDYNKVKLYEHAKAHSGLPRLAK

Source Source

Source organism organism	Favia favus
NCBI taxonomy ID ncbi_taxonomy_id	102203
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	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	600

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ddda_
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	d2dddb_
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 (2 domains)

Domain ID domain_id	2dddA00
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	2dddB00
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	97.837 Å
Unit-cell length b length_b	118.410 Å
Unit-cell length c length_c	48.856 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	—
R_work r_work	0.1750
R_free r_free	0.1900

Unique behavior of a histidine responsible for an engineered green-to-red photoconversion process

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

photoconvertible fluorescent protein

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

2ddd__assembly_1__model_1

2ddd__assembly_1__model_1 | I(q)

2ddd__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Unique behavior of a histidine responsible for an engineered green-to-red photoconversion process

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

photoconvertible fluorescent protein

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

2ddd__assembly_1__model_1

2ddd__assembly_1__model_1 | I(q)

2ddd__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)