SAXSdb — 1hmd

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

HEMERYTHRIN

Themiste dyscritum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	ACETYL GROUP × 8 MU-OXO-DIIRON × 8 water × 8	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ACETYL GROUP × 2 MU-OXO-DIIRON × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	ACETYL GROUP × 8 MU-OXO-DIIRON × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HEMT_THEDY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–113； UniProt 1–113 Author chain B； PDBConstruct 1–113； UniProt 1–113 Author chain C； PDBConstruct 1–113； UniProt 1–113 Author chain D； PDBConstruct 1–113； UniProt 1–113

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	1hmd
Deposition date deposition_date	1990-10-18
Structure title title	THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION
Keywords keywords	OXYGEN TRANSPORT; OXYGEN TRANSPORT
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.

1hmd__assembly_1__model_1

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

Download this curve (.dat)

1hmd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1hmd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.20 Å
Rg (electron density)	29.37 Å
Total Rg	30.01 Å
Atom count	7616
Residues	904
Excluded volume	134540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1hmd__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1hmd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1hmd__assembly_3__model_1`	octameric （8）	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	HEMERYTHRIN
Molecular weight formula_weight	13369.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4125

GFPIPDPYCWDISFRTFYTIIDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQSSQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKI

Source Source

Source organism organism	Themiste dyscritum
NCBI taxonomy ID ncbi_taxonomy_id	6436

Entity 2 Entity 2 non-polymer

Description description	ACETYL GROUP
Molecular weight formula_weight	44.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MU-OXO-DIIRON
Molecular weight formula_weight	127.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	293

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1hmda_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.4 — Hemerythrin-like
Family Family family	a.24.4.1 — Hemerythrin-like

Domain ID domain_id	d1hmdb_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.4 — Hemerythrin-like
Family Family family	a.24.4.1 — Hemerythrin-like

Domain ID domain_id	d1hmdc_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.4 — Hemerythrin-like
Family Family family	a.24.4.1 — Hemerythrin-like

Domain ID domain_id	d1hmdd_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.4 — Hemerythrin-like
Family Family family	a.24.4.1 — Hemerythrin-like

CATH v4.4 (4 domains)

Domain ID domain_id	1hmdA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	50 — Hemerythrin-like

Domain ID domain_id	1hmdB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	50 — Hemerythrin-like

Domain ID domain_id	1hmdC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	50 — Hemerythrin-like

Domain ID domain_id	1hmdD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	50 — Hemerythrin-like

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7. Citations (12)

Structures of deoxy and oxy hemerythrin at 2.0 A resolution.

J.Mol.Biol. (1991)

PMID: 2016748 · DOI: 10.1016/0022-2836(91)90703-9 PRIMARY

Active Site Structures of Deoxyhemerythrin and Oxyhemerythrin

Proc.Natl.Acad.Sci.USA (1985)

Binuclear Iron Complexes in Methemerythrin and Azidomethemerythrin at 2.0-Angstroms Resolution

J.Am.Chem.Soc. (1984)

Adjustment of Restraints in the Refinement of Methemerythrin and Azidomethemerythrin at 2.0 Angstroms Resolution.

Acta Crystallogr.,Sect.B (1983)

Restrained Least-Squares Refinement of Themiste Dyscritum Methydroxohemerythrin at 2.0 Angstroms Resolution

Acta Crystallogr.,Sect.B (1982)

Structure of the Binuclear Iron Complex in Metazidohaemerythrin from Themiste Dyscritum at 2.2 Angstroms Resolution

Nature (1981)

Amino Acid Sequence of Hemerythrin from Themiste Dyscritum.

J.Biol.Chem. (1978)

Crystallographic Studies of Azide, Thiocyanate and Perchlorate Complexes of Methemerythrin

J.Mol.Biol. (1978)

Structure of Methemerythrin at 2.8-Angstroms Resolution. Computer Graphics Fit of an Averaged Electron Density Map

Biochemistry (1978)

Structure of the Iron Complex in Methemerythrin

Proc.Natl.Acad.Sci.USA (1976)

Structure of Methemerythrin at 5 Angstroms Resolution

J.Mol.Biol. (1976)

An X-Ray Crystallographic Study of Hemerythrin

J.Mol.Biol. (1975)

Unit-cell length a length_a	86.840 Å
Unit-cell length b length_b	86.840 Å
Unit-cell length c length_c	80.820 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 4
Space-group number int_tables_number	75
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1680
R_work r_work	—
R_free r_free	—

THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION

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

HEMERYTHRIN

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

1hmd__assembly_1__model_1

1hmd__assembly_1__model_1 | I(q)

1hmd__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

Source Source

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 (12)

THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION

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

HEMERYTHRIN

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

1hmd__assembly_1__model_1

1hmd__assembly_1__model_1 | I(q)

1hmd__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

Source Source

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 (12)