SAXSdb — 2oqm

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

Hypothetical protein

Shewanella denitrificans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 10 FORMIC ACID × 15 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 7 FORMIC ACID × 9 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q12RS4_SHEDO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–192； UniProt 1–173 Author chain B； PDBConstruct 20–192； UniProt 1–173 Author chain C； PDBConstruct 20–192； UniProt 1–173 Author chain D； PDBConstruct 20–192； UniProt 1–173

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	2oqm
Deposition date deposition_date	2007-01-31
Structure title title	Crystal structure of a dinb family member protein (sden_0562) from shewanella denitrificans at 1.83 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.

2oqm__assembly_1__model_1

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

Download this curve (.dat)

2oqm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2oqm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.20 Å
Rg (electron density)	20.04 Å
Total Rg	20.88 Å
Atom count	2891
Residues	350
Excluded volume	51803 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2oqm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2oqm__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 (5)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein
Molecular weight formula_weight	21956.3 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	6349

MGSDKIHHHHHHENLYFQGMLYDLTVVQFSKMLKNLNAIFDKAEAFAELKKVDMDVLLNSRLAADQFNLIRQVQIACDTAKVGVARLTGQLETAPKHDDSETTLAELRQRIASVLTYLEGFSEADFANAATIQISQPRWQGKYLTGYEFAIEHAIPNLYFHITTAYGILRHNGVEVGKKDYLGAMPYKAPIL

Source Source

Source organism organism	Shewanella denitrificans
NCBI taxonomy ID ncbi_taxonomy_id	192073
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	24

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	545

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2oqma1
Class class	a — All alpha proteins
Fold Fold fold	a.213 — DinB/YfiT-like putative metalloenzymes
Superfamily Superfamily superfamily	a.213.1 — DinB/YfiT-like putative metalloenzymes
Family Family family	a.213.1.3 — Sden0562-like

Domain ID domain_id	d2oqma2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2oqmb2
Class class	a — All alpha proteins
Fold Fold fold	a.213 — DinB/YfiT-like putative metalloenzymes
Superfamily Superfamily superfamily	a.213.1 — DinB/YfiT-like putative metalloenzymes
Family Family family	a.213.1.3 — Sden0562-like

Domain ID domain_id	d2oqmb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2oqmc2
Class class	a — All alpha proteins
Fold Fold fold	a.213 — DinB/YfiT-like putative metalloenzymes
Superfamily Superfamily superfamily	a.213.1 — DinB/YfiT-like putative metalloenzymes
Family Family family	a.213.1.3 — Sden0562-like

Domain ID domain_id	d2oqmc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2oqmd2
Class class	a — All alpha proteins
Fold Fold fold	a.213 — DinB/YfiT-like putative metalloenzymes
Superfamily Superfamily superfamily	a.213.1 — DinB/YfiT-like putative metalloenzymes
Family Family family	a.213.1.3 — Sden0562-like

Domain ID domain_id	d2oqmd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2oqmA01
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	450 — dinb family like domain

Domain ID domain_id	2oqmB01
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	450 — dinb family like domain

Domain ID domain_id	2oqmC01
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	450 — dinb family like domain

Domain ID domain_id	2oqmD01
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	450 — dinb family like domain

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Unit-cell length a length_a	62.437 Å
Unit-cell length b length_b	71.722 Å
Unit-cell length c length_c	93.489 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.830 Å
Low-resolution limit resolution_low	45.220 Å
R factor r_factor	0.1590
R_work r_work	0.1570
R_free r_free	0.1960

Crystal structure of a dinb family member protein (sden_0562) from shewanella denitrificans at 1.83 A resolution

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

Hypothetical protein

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

2oqm__assembly_1__model_1

2oqm__assembly_1__model_1 | I(q)

2oqm__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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a dinb family member protein (sden_0562) from shewanella denitrificans at 1.83 A resolution

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

Hypothetical protein

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

2oqm__assembly_1__model_1

2oqm__assembly_1__model_1 | I(q)

2oqm__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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)