SAXSdb — 3k3u

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

Dehaloperoxidase A

Amphitrite ornata

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 SULFATE ION × 6 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PROTOPORPHYRIN IX CONTAINING FE × 2 SULFATE ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9NAV8_9ANNE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–137； UniProt 2–138 Author chain B； PDBConstruct 1–137； UniProt 2–138

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	3k3u
Deposition date deposition_date	2009-10-05
Structure title title	The V59W mutation blocks the distal pocket of the hemoglobin dehaloperoxidase from Amphitrite ornata
Keywords keywords	peroxidase, globin, Heme, Oxygen transport, Transport, 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.

3k3u__assembly_1__model_1

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

Download this curve (.dat)

3k3u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3k3u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.77 Å
Rg (electron density)	24.34 Å
Total Rg	24.99 Å
Atom count	2284
Residues	273
Excluded volume	40317 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3k3u__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3k3u__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Dehaloperoxidase A
Molecular weight formula_weight	15635.7 kDa
Mutation mutation	V59W
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	3504

GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMAKFGDHTEKWFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLFVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK

Source Source

Source organism organism	Amphitrite ornata
NCBI taxonomy ID ncbi_taxonomy_id	129555
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	410

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3k3ua_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.2 — Globins

Domain ID domain_id	d3k3ub_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.2 — Globins

CATH v4.4 (2 domains)

Domain ID domain_id	3k3uA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	3k3uB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

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Unit-cell length a length_a	57.766 Å
Unit-cell length b length_b	67.321 Å
Unit-cell length c length_c	69.462 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.630 Å
Low-resolution limit resolution_low	30.290 Å
R factor r_factor	0.1700
R_work r_work	0.1684
R_free r_free	0.2012

The V59W mutation blocks the distal pocket of the hemoglobin dehaloperoxidase from Amphitrite ornata

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

Dehaloperoxidase A

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

3k3u__assembly_1__model_1

3k3u__assembly_1__model_1 | I(q)

3k3u__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The V59W mutation blocks the distal pocket of the hemoglobin dehaloperoxidase from Amphitrite ornata

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

Dehaloperoxidase A

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

3k3u__assembly_1__model_1

3k3u__assembly_1__model_1 | I(q)

3k3u__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)