SAXSdb — 1v8x

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

Heme oxygenase

Corynebacterium diphtheriae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 3 OXYGEN MOLECULE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 4 OXYGEN MOLECULE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 SULFATE ION × 5 OXYGEN MOLECULE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMUO_CORDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–215； UniProt 1–215 Author chain B； PDBConstruct 1–215； UniProt 1–215 Author chain C； 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	1v8x
Deposition date deposition_date	2004-01-15
Structure title title	Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae
Keywords keywords	PROTEIN-HEME COMPLEX, HELIX, OXY, 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.

1v8x__assembly_1__model_1

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

Download this curve (.dat)

1v8x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1v8x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.96 Å
Rg (electron density)	16.53 Å
Total Rg	17.63 Å
Atom count	1751
Residues	210
Excluded volume	30801 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1v8x__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1v8x__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1v8x__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	Heme oxygenase
Molecular weight formula_weight	24170.2 kDa
EC 编号 ec_number	1.14.99.3
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5679

MTTATAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL

Source Source

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

Entity 2 Entity 2 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

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	3

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	449

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1v8xa_
Class class	a — All alpha proteins
Fold Fold fold	a.132 — Heme oxygenase-like
Superfamily Superfamily superfamily	a.132.1 — Heme oxygenase-like
Family Family family	a.132.1.1 — Eukaryotic type heme oxygenase

Domain ID domain_id	d1v8xb_
Class class	a — All alpha proteins
Fold Fold fold	a.132 — Heme oxygenase-like
Superfamily Superfamily superfamily	a.132.1 — Heme oxygenase-like
Family Family family	a.132.1.1 — Eukaryotic type heme oxygenase

Domain ID domain_id	d1v8xc_
Class class	a — All alpha proteins
Fold Fold fold	a.132 — Heme oxygenase-like
Superfamily Superfamily superfamily	a.132.1 — Heme oxygenase-like
Family Family family	a.132.1.1 — Eukaryotic type heme oxygenase

CATH v4.4 (3 domains)

Domain ID domain_id	1v8xA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	910 — Heme Oxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Heme oxygenase-like

Domain ID domain_id	1v8xB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	910 — Heme Oxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Heme oxygenase-like

Domain ID domain_id	1v8xC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	910 — Heme Oxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Heme oxygenase-like

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Unit-cell length a length_a	54.003 Å
Unit-cell length b length_b	62.969 Å
Unit-cell length c length_c	107.490 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1570
R_work r_work	0.1530
R_free r_free	0.1925

Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae

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

Heme oxygenase

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

1v8x__assembly_1__model_1

1v8x__assembly_1__model_1 | I(q)

1v8x__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae

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

Heme oxygenase

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

1v8x__assembly_1__model_1

1v8x__assembly_1__model_1 | I(q)

1v8x__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)