SAXSdb — 2oyy

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

Hexameric cytochrome

Silicibacter pomeroyi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	IODIDE ION × 9 PROTOPORPHYRIN IX CONTAINING FE × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	IODIDE ION × 9 PROTOPORPHYRIN IX CONTAINING FE × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 24	IODIDE ION × 36 PROTOPORPHYRIN IX CONTAINING FE × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LL55_SILPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain C； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain E； PDBConstruct 1–76； UniProt 1–76 Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain G； PDBConstruct 1–76； UniProt 1–76 Author chain H； PDBConstruct 1–76； UniProt 1–76

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	2oyy
Deposition date deposition_date	2007-02-23
Structure title title	HTHP: a hexameric tyrosine-coordinated heme protein
Keywords keywords	all helical, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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.

2oyy__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2oyy__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2oyy__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.08 Å
Rg (electron density)	20.81 Å
Total Rg	21.80 Å
Atom count	3549
Residues	426
Excluded volume	63919 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2oyy__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2oyy__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2oyy__assembly_3__model_1`	24-meric （24）	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 (3)

Entity 1 Entity 1 polymer

Description description	Hexameric cytochrome
Molecular weight formula_weight	8370.5 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	4732

MSETWLPTLVTATPQEGFDLAVKLSRIAVKKTQPDAQVRDTLRAVYEKDANALIAVSAVVATHFQTIAAANDYWKD

Source Source

Source organism organism	Silicibacter pomeroyi
NCBI taxonomy ID ncbi_taxonomy_id	89184
Host organism host_organism	Escherichia coli K12

Entity 2 Entity 2 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2oyyA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	80 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Hexameric tyrosine-coordinated heme protein (HTHP)

Domain ID domain_id	2oyyB00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	80 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Hexameric tyrosine-coordinated heme protein (HTHP)

Domain ID domain_id	2oyyC00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	80 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Hexameric tyrosine-coordinated heme protein (HTHP)

Domain ID domain_id	2oyyD00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	80 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Hexameric tyrosine-coordinated heme protein (HTHP)

Domain ID domain_id	2oyyE00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	80 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Hexameric tyrosine-coordinated heme protein (HTHP)

Domain ID domain_id	2oyyF00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	80 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Hexameric tyrosine-coordinated heme protein (HTHP)

Domain ID domain_id	2oyyG00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	80 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Hexameric tyrosine-coordinated heme protein (HTHP)

Domain ID domain_id	2oyyH00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	80 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	10 — Hexameric tyrosine-coordinated heme protein (HTHP)

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Unit-cell length a length_a	173.710 Å
Unit-cell length b length_b	173.710 Å
Unit-cell length c length_c	45.880 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	72

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	86.710 Å
R factor r_factor	0.2360
R_work r_work	0.2342
R_free r_free	0.2687

HTHP: a hexameric tyrosine-coordinated heme protein

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

Hexameric cytochrome

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

2oyy__assembly_2__model_1

2oyy__assembly_2__model_1 | I(q)

2oyy__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

HTHP: a hexameric tyrosine-coordinated heme protein

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

Hexameric cytochrome

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

2oyy__assembly_2__model_1

2oyy__assembly_2__model_1 | I(q)

2oyy__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)