SAXSdb — 2nwb

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

Conserved domain protein

Shewanella oneidensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8E972_SHEON
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–392； UniProt 1–392 Author chain B； PDBConstruct 1–392； UniProt 1–392

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	2nwb
Deposition date deposition_date	2006-11-14
Structure title title	Crystal Structure of a Putative 2,3-dioxygenase (SO4414) from Shewanella oneidensis in complex with ferric heme. Northeast Structural Genomics Target SoR52.
Keywords keywords	;Dioxygenase, Heme-binding protein, Hemoprotein, all alpha-helical protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

2nwb__assembly_1__model_1

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

Download this curve (.dat)

2nwb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nwb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.84 Å
Rg (electron density)	33.87 Å
Total Rg	34.43 Å
Atom count	12182
Residues	1488
Excluded volume	215770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nwb__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 (3)

Entity 1 Entity 1 polymer

Description description	Conserved domain protein
Molecular weight formula_weight	46110.2 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	6398

MKPATYNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYMAACRRHEITEPTRETTSPLLEASALAMHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQMLVDKFLYMMPEDQQILRECMRRPNLMDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKYIAEPSVSMEQQHLAKVTASGPPLHVLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLRLEHHHHHH

Source Source

Source organism organism	Shewanella oneidensis
NCBI taxonomy ID ncbi_taxonomy_id	211586
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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	307

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2nwba1
Class class	a — All alpha proteins
Fold Fold fold	a.266 — Indolic compounds 2,3-dioxygenase-like
Superfamily Superfamily superfamily	a.266.1 — Indolic compounds 2,3-dioxygenase-like
Family Family family	a.266.1.2 — Indoleamine 2,3-dioxygenase-like

Domain ID domain_id	d2nwba2
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	d2nwbb1
Class class	a — All alpha proteins
Fold Fold fold	a.266 — Indolic compounds 2,3-dioxygenase-like
Superfamily Superfamily superfamily	a.266.1 — Indolic compounds 2,3-dioxygenase-like
Family Family family	a.266.1.2 — Indoleamine 2,3-dioxygenase-like

Domain ID domain_id	d2nwbb2
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	2nwbA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	600 —

Domain ID domain_id	2nwbA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	480 —

Domain ID domain_id	2nwbB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	600 —

Domain ID domain_id	2nwbB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	480 —

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Unit-cell length a length_a	138.851 Å
Unit-cell length b length_b	68.698 Å
Unit-cell length c length_c	87.790 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	2.400 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2250

Crystal Structure of a Putative 2,3-dioxygenase (SO4414) from Shewanella oneidensis in complex with ferric heme. Northeast Structural Genomics Target SoR52.

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

Conserved domain 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

2nwb__assembly_1__model_1

2nwb__assembly_1__model_1 | I(q)

2nwb__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of a Putative 2,3-dioxygenase (SO4414) from Shewanella oneidensis in complex with ferric heme. Northeast Structural Genomics Target SoR52.

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

Conserved domain 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

2nwb__assembly_1__model_1

2nwb__assembly_1__model_1 | I(q)

2nwb__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)