SAXSdb — 9fyh

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

Deferrochelatase

Streptomyces lividans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PROTOPORPHYRIN IX CONTAINING FE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7U9DT46_STRLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–373； UniProt 48–420 Author chain B； PDBConstruct 1–373； UniProt 48–420

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	9fyh
Deposition date deposition_date	2024-07-03
Structure title title	Dye Type Peroxidase Aa from Streptomyces lividans by microcrystal electron diffraction (MicroED/3D ED)
Keywords keywords	microcrystal electron diffraction, MicroED, 3D ED, DPtAa, oxireductase, heme, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	ELECTRON CRYSTALLOGRAPHY

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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.

9fyh__assembly_1__model_1

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

Download this curve (.dat)

9fyh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9fyh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.30 Å
Rg (electron density)	26.35 Å
Total Rg	27.20 Å
Atom count	11162
Residues	729
Excluded volume	99609 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9fyh__assembly_1__model_1`	dimeric （2）	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	Deferrochelatase
Molecular weight formula_weight	40240.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11393

DPAGADAGSAVPFHGAHQAGIATPVQDRLHFAAFDVTTEDRAAFVALLKEWTAAARRLTAGHAVGEGAYGGLPEAPPDDTGEALGLKPSRLTLTIGFGPSLFTRFGLADLRPEALADLPKFPGDNLDRARSGGDLCVQACADDPQVAVHAIRNLARIGFGKVVVRWSQLGFGKTSSTTPDKQTPRNLLGFKDGTRNIAGTEKDRLDRFVWAAEKDGTPWMTGGSYLVARRIRMHIETWDRASLQEQEDVFGRDKGEGAPVGKAKERDEPFLKAMKPDAHVRLAHPDSNGGATLLRRGYSFTDGTDGLGRLDAGLFFLAYQRDIRTGFVPVQRNLATDALNEFIQHVGSAVFAVPPGVRDADDWWGSTLFGKEA

Source Source

Source organism organism	Streptomyces lividans
NCBI taxonomy ID ncbi_taxonomy_id	1916
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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Unit-cell length a length_a	72.770 Å
Unit-cell length b length_b	67.400 Å
Unit-cell length c length_c	73.630 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.460 Å
R factor r_factor	0.2053
R_work r_work	0.2019
R_free r_free	0.2561

Resolution resolution	2.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	—

Dye Type Peroxidase Aa from Streptomyces lividans by microcrystal electron diffraction (MicroED/3D ED)

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

Deferrochelatase

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

9fyh__assembly_1__model_1

9fyh__assembly_1__model_1 | I(q)

9fyh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

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

7. Citations (1)

Dye Type Peroxidase Aa from Streptomyces lividans by microcrystal electron diffraction (MicroED/3D ED)

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

Deferrochelatase

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

9fyh__assembly_1__model_1

9fyh__assembly_1__model_1 | I(q)

9fyh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

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

7. Citations (1)