SAXSdb — 5exc

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

Green fluorescent protein

Dendronephthya sp. SSAL-2002

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	GLYCEROL × 1 MAGNESIUM ION × 7 water × 8	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	GLYCEROL × 2 MAGNESIUM ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8T6U0_9CNID
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 3–62； UniProt 2–61 Author chain B； PDBConstruct 3–62； UniProt 2–61 Author chain C； PDBConstruct 3–62； UniProt 2–61 Author chain D； PDBConstruct 3–62； UniProt 2–61 Author chain E； PDBConstruct 3–62； UniProt 2–61 Author chain F； PDBConstruct 3–62； UniProt 2–61 Author chain G； PDBConstruct 3–62； UniProt 2–61 Author chain H； PDBConstruct 3–62； UniProt 2–61 Author chain aa； PDBConstruct 1–162； UniProt 62–225 Author chain bb； PDBConstruct 1–162； UniProt 62–225 Author chain cc； PDBConstruct 1–162； UniProt 62–225 Author chain dd； PDBConstruct 1–162； UniProt 62–225 Author chain ee； PDBConstruct 1–162； UniProt 62–225 Author chain ff； PDBConstruct 1–162； UniProt 62–225 Author chain gg； PDBConstruct 1–162； UniProt 62–225 Author chain hh； PDBConstruct 1–162； UniProt 62–225

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	5exc
Deposition date deposition_date	2015-11-23
Structure title title	Photoconverted red fluorescent protein DendRFP
Keywords keywords	Photoswitchable fluorescent proteins, chromophore, beta-barrel, biomarker, 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.

5exc__assembly_1__model_1

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

Download this curve (.dat)

5exc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5exc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.19 Å
Rg (electron density)	28.25 Å
Total Rg	29.08 Å
Atom count	7279
Residues	884
Excluded volume	129350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5exc__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5exc__assembly_2__model_1`	octameric （8）	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 (5)

Entity 1 Entity 1 polymer

Description description	Green fluorescent protein
Molecular weight formula_weight	6767.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	15333

MGNLIKEDMRVKVHMEGNVNGHAFVIEGEGKGKPYEGTQTLNLTVKEGAPLPFSYDILTTAL

Source Source

Source organism organism	Dendronephthya sp. SSAL-2002
NCBI taxonomy ID ncbi_taxonomy_id	191210
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Green fluorescent protein
Molecular weight formula_weight	20085.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	aa,bb,cc,dd,ee,ff,gg,hh

XNRVFTKYPEDIPDYFKQSFPEGYSWERTMTYEDKGICTIRSDISLEGDCFFQNVRFNGMNFPPNGPVMQKKTLKWEPSTEKLHVRDGLLVGNINMALLLEGGGHYLCDFKTTYKAKKVVQLPDYHFVDHRIEILSNDSDYNKVKLYEHGVARYSPLPSQAWGSHHHHHH

Source Source

Source organism organism	Dendronephthya sp. SSAL-2002
NCBI taxonomy ID ncbi_taxonomy_id	191210
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	643

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Unit-cell length a length_a	57.423 Å
Unit-cell length b length_b	69.521 Å
Unit-cell length c length_c	124.481 Å
Unit-cell angle α angle_alpha	89.88 °
Unit-cell angle β angle_beta	89.94 °
Unit-cell angle γ angle_gamma	65.57 °
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	2.140 Å
Low-resolution limit resolution_low	29.870 Å
R factor r_factor	0.1961
R_work r_work	0.1945
R_free r_free	0.2793

Photoconverted red fluorescent protein DendRFP

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

Green 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

5exc__assembly_1__model_1

5exc__assembly_1__model_1 | I(q)

5exc__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Photoconverted red fluorescent protein DendRFP

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

Green 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

5exc__assembly_1__model_1

5exc__assembly_1__model_1 | I(q)

5exc__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)