SAXSdb — 9fy4

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

heme oxygenase (biliverdin-producing)

Corynebacterium diphtheriae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 PROTOPORPHYRIN IX CONTAINING CO × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING CO × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q54AI1_CORDP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–215； UniProt 1–215 Author chain H； PDBConstruct 1–215； UniProt 1–215

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	9fy4
Deposition date deposition_date	2024-07-02
Last revision last_revision	2024-10-16
Structure title title	Crystal structure of Heme-Oxygenase mutant I143K from Corynebacterium diphtheriae complexed with Cobalt-porphyrine (HumO-Co(III))
Keywords keywords	carbon dioxide photo-reduction artificial-enzyme cobalt-porphyrin heme-oxygenase oxidoreductase, 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.

9fy4__assembly_1__model_1

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

Download this curve (.dat)

9fy4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9fy4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.16 Å
Rg (electron density)	16.65 Å
Total Rg	17.83 Å
Atom count	1706
Residues	209
Excluded volume	30184 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9fy4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9fy4__assembly_2__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	heme oxygenase (biliverdin-producing)
Molecular weight formula_weight	24186.2 kDa
EC 编号 ec_number	1.14.14.18
Mutation mutation	I143K
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H
Atom count atom_count	3532

MTTATAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVKARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL

Source Source

Source organism organism	Corynebacterium diphtheriae
NCBI taxonomy ID ncbi_taxonomy_id	1717
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING CO
Molecular weight formula_weight	619.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

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Unit-cell length a length_a	41.681 Å
Unit-cell length b length_b	63.525 Å
Unit-cell length c length_c	76.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.37 °
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	2.839 Å
Low-resolution limit resolution_low	48.610 Å
R factor r_factor	0.2372
R_work r_work	0.2340
R_free r_free	0.3061

Crystal structure of Heme-Oxygenase mutant I143K from Corynebacterium diphtheriae complexed with Cobalt-porphyrine (HumO-Co(III))

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

heme oxygenase (biliverdin-producing)

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

9fy4__assembly_1__model_1

9fy4__assembly_1__model_1 | I(q)

9fy4__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of Heme-Oxygenase mutant I143K from Corynebacterium diphtheriae complexed with Cobalt-porphyrine (HumO-Co(III))

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

heme oxygenase (biliverdin-producing)

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

9fy4__assembly_1__model_1

9fy4__assembly_1__model_1 | I(q)

9fy4__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)