SAXSdb — 3dde

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

TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold

Shewanella denitrificans OS217

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	DI(HYDROXYETHYL)ETHER × 6 NITRATE ION × 2 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q12HR3_SHEDO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–239； UniProt 1–238 Author chain B； PDBConstruct 2–239； UniProt 1–238

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	3dde
Deposition date deposition_date	2008-06-05
Structure title title	Crystal structure of a domain of unknown function with a heme oxygenase-like fold (sden_3740) from shewanella denitrificans os217 at 2.30 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function; UNKNOWN FUNCTION
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.

3dde__assembly_1__model_1

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

Download this curve (.dat)

3dde__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dde__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.57 Å
Rg (electron density)	29.68 Å
Total Rg	30.29 Å
Atom count	7188
Residues	898
Excluded volume	128360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dde__assembly_1__model_1`	tetrameric （4）	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	TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold
Molecular weight formula_weight	27380.8 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	3753

GMSIIDLTKLEQKVATMWDSILTNSPFIHEVLDGKATKALYAIYMTETYHYTKHNAKNQALVGIMGKDLPGKYLSFCFHHAHEEAGHELMALSDIASIGFDREDVLSSKPLPATETLIAYLYWISATGNPVQRLGYSYWAENVYGYIDPVLKAIQSTLDLTPQSMKFFIAHSKIDAKHAEEVNEMLHEVCKTQEDVDSVVAVMENSLVLTARILDDVWKEYQLFQSGASDRYAFLRDNA

Source Source

Source organism organism	Shewanella denitrificans OS217
NCBI taxonomy ID ncbi_taxonomy_id	318161
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	74

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3ddeA00
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	3ddeB00
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	92.810 Å
Unit-cell length b length_b	66.000 Å
Unit-cell length c length_c	84.380 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.173 Å
R factor r_factor	0.2210
R_work r_work	0.2200
R_free r_free	0.2530

Crystal structure of a domain of unknown function with a heme oxygenase-like fold (sden_3740) from shewanella denitrificans os217 at 2.30 A resolution

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

TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold

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

3dde__assembly_1__model_1

3dde__assembly_1__model_1 | I(q)

3dde__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 non-polymer

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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a domain of unknown function with a heme oxygenase-like fold (sden_3740) from shewanella denitrificans os217 at 2.30 A resolution

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

TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold

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

3dde__assembly_1__model_1

3dde__assembly_1__model_1 | I(q)

3dde__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 non-polymer

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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)