SAXSdb — 4zl5

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

Ferritin

Pseudo-nitzschia multiseries

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 24	FE (III) ION × 96 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B6DMH6_9STRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–169； UniProt 63–230 Author chain B； PDBConstruct 2–169； UniProt 63–230 Author chain C； PDBConstruct 2–169； UniProt 63–230 Author chain D； PDBConstruct 2–169； UniProt 63–230 Author chain E； PDBConstruct 2–169； UniProt 63–230 Author chain F； PDBConstruct 2–169； UniProt 63–230

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	4zl5
Deposition date deposition_date	2015-05-01
Structure title title	Crystal structure of the PmFTN variant E44H soaked in iron (45 min)
Keywords keywords	ferritin, di-iron ferroxidase centre, 4-helix bundle, 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.

4zl5__assembly_1__model_1

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

Download this curve (.dat)

4zl5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4zl5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.56 Å
Rg (electron density)	52.50 Å
Total Rg	52.88 Å
Atom count	30100
Residues	3768
Excluded volume	531150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4zl5__assembly_1__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	Ferritin
Molecular weight formula_weight	18975.1 kDa
EC 编号 ec_number	1.16.3.1
Mutation mutation	E44H
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D,E,F
Atom count atom_count	8402

GSEELLDLFNRQVTQEFTASQVYLSASIWFDQNDWEGMAAYMLAHSAEEREHGLGFVDFANKRNIPIELQAVPAPVSCAEWSSPEDVWQSILELEQANTRSLLNLAEAASTCHDFAVMAFLNPFHLQQVNEEDKIGSILAKVTDENRTPGLLRSLDVVSFLGPCLFRSV

Source Source

Source organism organism	Pseudo-nitzschia multiseries
NCBI taxonomy ID ncbi_taxonomy_id	37319
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	699

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4zl5a_
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.25.1.0 — automated matches

Domain ID domain_id	d4zl5b_
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.25.1.0 — automated matches

Domain ID domain_id	d4zl5c_
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.25.1.0 — automated matches

Domain ID domain_id	d4zl5d_
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.25.1.0 — automated matches

Domain ID domain_id	d4zl5e_
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.25.1.0 — automated matches

Domain ID domain_id	d4zl5f_
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.25.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	4zl5A00
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	4zl5B00
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	4zl5C00
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	4zl5D00
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	4zl5E00
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	4zl5F00
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

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Unit-cell length a length_a	126.460 Å
Unit-cell length b length_b	126.460 Å
Unit-cell length c length_c	170.310 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	48

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	47.930 Å
R factor r_factor	0.1739
R_work r_work	0.1722
R_free r_free	0.2069

Crystal structure of the PmFTN variant E44H soaked in iron (45 min)

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

Ferritin

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

4zl5__assembly_1__model_1

4zl5__assembly_1__model_1 | I(q)

4zl5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the PmFTN variant E44H soaked in iron (45 min)

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

Ferritin

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

4zl5__assembly_1__model_1

4zl5__assembly_1__model_1 | I(q)

4zl5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)