SAXSdb — 1s36

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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	SODIUM ION × 1 CHLORIDE ION × 1 N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE × 1 GLYCEROL × 1 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

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	1s36
Deposition date deposition_date	2004-01-12
Structure title title	Crystal structure of a Ca2+-discharged photoprotein: Implications for the mechanisms of the calcium trigger and the bioluminescence
Keywords keywords	;Photoprotein, obelin, bioluminescence, calcium binding, EF-hand, aequorin, Structural Genomics, PSI, Protein Structure Initiative, Southeast Collaboratory for Structural Genomics, SECSG, 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.

1s36__assembly_1__model_1

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

Download this curve (.dat)

1s36__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1s36__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.98 Å
Rg (electron density)	15.52 Å
Total Rg	16.72 Å
Atom count	1528
Residues	185
Excluded volume	26968 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1s36__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Obelin
Molecular weight formula_weight	22215.9 kDa
Mutation mutation	W92F
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1677

MSSKYAVKLKTDFDNPRWIKRHKHMFDFLDINGNGKITLDEIVSKASDDICAKLEATPEQTKRHQVCVEAFFRGCGMEYGKEIAFPQFLDGFKQLATSELKKWARNEPTLIREWGDAVFDIFDKDGSGTITLDEWKAYGKISGISPSQEDCEATFRHCDLDNSGDLDVDEMTRQHLGFWYTLDPEADGLYGNGVP

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE
Molecular weight formula_weight	411.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1s36a_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

CATH v4.4 (1 domains)

Domain ID domain_id	1s36A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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7. Citations (7)

Crystal structure of a Ca2+-discharged photoprotein: implications for mechanisms of the calcium trigger and bioluminescence

J.Biol.Chem. (2004)

PMID: 15155735 · DOI: 10.1074/jbc.M402427200 PRIMARY

;Violet Bioluminescence and Fast Kinetics from W92F Obelin: Structure-Based Proposals for the Bioluminescence Triggering and the Identification of the Emitting Species ;

Biochemistry (2003)

;Atomic resolution structure of obelin: Soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine ;

Biochem.Biophys.Res.Commun. (2003)

;Structural basis for the emission of violet bioluminescence from a W92F obelin mutant ;

FEBS Lett. (2001)

Structure of the Ca2+-regulated photoprotein obelin at 1.7 resolution determined directly from its sulfur substructure

Protein Sci. (2000)

;Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima ;

Acta Crystallogr.,Sect.D (1999)

;Preparation and X-ray Crystallographic Analysis of the Ca2+-discharged Photoprotein Obelin ;

To be Published

Unit-cell length a length_a	53.445 Å
Unit-cell length b length_b	53.445 Å
Unit-cell length c length_c	144.032 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2246
R_work r_work	0.2228
R_free r_free	0.2592

Crystal structure of a Ca2+-discharged photoprotein: Implications for the mechanisms of the calcium trigger and the bioluminescence

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

1s36__assembly_1__model_1

1s36__assembly_1__model_1 | I(q)

1s36__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (7)

Crystal structure of a Ca2+-discharged photoprotein: Implications for the mechanisms of the calcium trigger and the bioluminescence

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

1s36__assembly_1__model_1

1s36__assembly_1__model_1 | I(q)

1s36__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (7)