SAXSdb — 8a9s

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

Obelin

Obelia longissima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	3-azanyl-2-(phenylmethyl)benzo[f]quinoxalin-8-ol × 1 SODIUM ION × 1 DIMETHYL SULFOXIDE × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	3-azanyl-2-(phenylmethyl)benzo[f]quinoxalin-8-ol × 1 SODIUM ION × 1 DIMETHYL SULFOXIDE × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OBL_OBELO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–195； UniProt 1–195 Author chain B； PDBConstruct 1–195； UniProt 1–195

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	8a9s
Deposition date deposition_date	2022-06-29
Structure title title	Crystal structure of Ca2+-discharged obelin in complex with coelenteramine-v
Keywords keywords	bioluminescence, photoprotein, obelin, coelenterazine analogue, coelenterazine-v, 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.

8a9s__assembly_1__model_1

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

Download this curve (.dat)

8a9s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8a9s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.51 Å
Rg (electron density)	16.16 Å
Total Rg	17.36 Å
Atom count	3051
Residues	192
Excluded volume	27724 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8a9s__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8a9s__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Obelin
Molecular weight formula_weight	22254.9 kDa
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	6526

MSSKYAVKLKTDFDNPRWIKRHKHMFDFLDINGNGKITLDEIVSKASDDICAKLEATPEQTKRHQVCVEAFFRGCGMEYGKEIAFPQFLDGWKQLATSELKKWARNEPTLIREWGDAVFDIFDKDGSGTITLDEWKAYGKISGISPSQEDCEATFRHCDLDNSGDLDVDEMTRQHLGFWYTLDPEADGLYGNGVP

Source Source

Source organism organism	Obelia longissima
NCBI taxonomy ID ncbi_taxonomy_id	32570
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	3-azanyl-2-(phenylmethyl)benzo[f]quinoxalin-8-ol
Molecular weight formula_weight	301.3 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 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	341

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Unit-cell length a length_a	77.281 Å
Unit-cell length b length_b	77.281 Å
Unit-cell length c length_c	182.224 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	hexagonal

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	33.460 Å
R factor r_factor	0.1606
R_work r_work	0.1595
R_free r_free	0.2103

Crystal structure of Ca2+-discharged obelin in complex with coelenteramine-v

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

Obelin

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

8a9s__assembly_1__model_1

8a9s__assembly_1__model_1 | I(q)

8a9s__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of Ca2+-discharged obelin in complex with coelenteramine-v

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

Obelin

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

8a9s__assembly_1__model_1

8a9s__assembly_1__model_1 | I(q)

8a9s__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)