SAXSdb — 3pza

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

Rubrerythrin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	HYDROGEN PEROXIDE × 2 FE (II) ION × 6 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	HYDROGEN PEROXIDE × 4 FE (II) ION × 12 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9UWP7_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–170； UniProt 2–171 Author chain B； PDBConstruct 1–170； UniProt 2–171

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	3pza
Deposition date deposition_date	2010-12-14
Structure title title	Fully Reduced (All-ferrous) Pyrococcus rubrerythrin after a 10 second exposure to peroxide.
Keywords keywords	Rubrerythrin, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

3pza__assembly_1__model_1

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

Download this curve (.dat)

3pza__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pza__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.09 Å
Rg (electron density)	20.21 Å
Total Rg	21.12 Å
Atom count	2736
Residues	340
Excluded volume	49234 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pza__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pza__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Rubrerythrin
Molecular weight formula_weight	19398.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2885

VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE

Entity 2 Entity 2 non-polymer

Description description	HYDROGEN PEROXIDE
Molecular weight formula_weight	34.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	131

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3pzaa1
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d3pzaa2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.0 — automated matches

Domain ID domain_id	d3pzab1
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.1 — Ferritin

Domain ID domain_id	d3pzab2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3pzaA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	3pzaA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3pzaB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	10 — Ferritin, core subunit, four-helix bundle

Domain ID domain_id	3pzaB02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	104.602 Å
Unit-cell length b length_b	104.602 Å
Unit-cell length c length_c	79.591 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	16

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	43.710 Å
R factor r_factor	0.1768
R_work r_work	0.1756
R_free r_free	0.1998

Fully Reduced (All-ferrous) Pyrococcus rubrerythrin after a 10 second exposure to peroxide.

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

Rubrerythrin

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

3pza__assembly_1__model_1

3pza__assembly_1__model_1 | I(q)

3pza__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Fully Reduced (All-ferrous) Pyrococcus rubrerythrin after a 10 second exposure to peroxide.

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

Rubrerythrin

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

3pza__assembly_1__model_1

3pza__assembly_1__model_1 | I(q)

3pza__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)