SAXSdb — 3bk6

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

PH stomatin

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1511_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–180； UniProt 56–234 Author chain B； PDBConstruct 2–180； UniProt 56–234 Author chain C； PDBConstruct 2–180； UniProt 56–234

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	3bk6
Deposition date deposition_date	2007-12-05
Structure title title	Crystal structure of a core domain of stomatin from Pyrococcus horikoshii
Keywords keywords	;stomatin, archaea, Pyrococcus horikoshii, trimer, coiled-coil, flotillin, SPFH, membrane fusion, trafficking, Transmembrane, MEMBRANE PROTEIN ;; MEMBRANE 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.

3bk6__assembly_1__model_1

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

Download this curve (.dat)

3bk6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bk6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.97 Å
Rg (electron density)	33.26 Å
Total Rg	33.66 Å
Atom count	3732
Residues	472
Excluded volume	66897 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bk6__assembly_1__model_1`	trimeric （3）	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 (1)

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	3bk6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	30 — Band 7 domain

Domain ID domain_id	3bk6A02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2090 —

Domain ID domain_id	3bk6B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	30 — Band 7 domain

Domain ID domain_id	3bk6C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	30 — Band 7 domain

Domain ID domain_id	3bk6C02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2090 —

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Unit-cell length a length_a	142.553 Å
Unit-cell length b length_b	137.150 Å
Unit-cell length c length_c	58.544 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.2045
R_work r_work	0.1977
R_free r_free	0.2623

Description description	PH stomatin
Molecular weight formula_weight	21297.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3732

Crystal structure of a core domain of stomatin from Pyrococcus horikoshii

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

PH stomatin

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

3bk6__assembly_1__model_1

3bk6__assembly_1__model_1 | I(q)

3bk6__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (2)

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Crystal structure of a core domain of stomatin from Pyrococcus horikoshii

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

PH stomatin

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

3bk6__assembly_1__model_1

3bk6__assembly_1__model_1 | I(q)

3bk6__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (2)