SAXSdb — 1xdq

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

Bacterial Sulfite Oxidase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	UREA × 1 MOLYBDENUM ATOM × 1 OXYGEN ATOM × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	UREA × 1 MOLYBDENUM ATOM × 1 OXYGEN ATOM × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	UREA × 1 MOLYBDENUM ATOM × 1 OXYGEN ATOM × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	UREA × 1 MOLYBDENUM ATOM × 1 OXYGEN ATOM × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	UREA × 1 MOLYBDENUM ATOM × 1 OXYGEN ATOM × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YEDY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–290； UniProt 45–334 Author chain B； PDBConstruct 1–290； UniProt 45–334 Author chain C； PDBConstruct 1–290； UniProt 45–334 Author chain D； PDBConstruct 1–290； UniProt 45–334 Author chain E； PDBConstruct 1–290； UniProt 45–334

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	1xdq
Deposition date deposition_date	2004-09-07
Structure title title	Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase
Keywords keywords	Bioinformatics, sequence analysis, electron transfer, oxidoreductase, molybdoenzymes, molybdopterin; 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.

1xdq__assembly_1__model_1

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

Download this curve (.dat)

1xdq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xdq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.42 Å
Rg (electron density)	17.22 Å
Total Rg	18.20 Å
Atom count	2115
Residues	262
Excluded volume	37694 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xdq__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xdq__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1xdq__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1xdq__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1xdq__assembly_5__model_1`	monomeric （1）	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	Bacterial Sulfite Oxidase
Molecular weight formula_weight	33666.3 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	10771

DLLSWFKGNDRPPAPAGKALEFSKPAAWQNNLPLTPADKVSGYNNFYEFGLDKADPAANAGSLKTDPWTLKISGEVAKPLTLDHDDLTRRFPLEERIYRMRCVEAWSMVVPWIGFPLHKLLALAEPTSNAKYVAFETIYAPEQMPGQQDRFIGGGLKYPYVEGLRLDEAMHPLTLMTVGVYGKALPPQNGAPVRLIVPWKYGFKGIKSIVSIKLTRERPPTTWNLAAPDEYGFYANVNPYVDHPRWSQATERFIGSGGILDVQRQPTLLFNGYADQVASLYRGLDLRENFLEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	UREA
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	MOLYBDENUM ATOM
Molecular weight formula_weight	95.9 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	OXYGEN ATOM
Molecular weight formula_weight	16.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
Molecular weight formula_weight	395.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1xdqa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

Domain ID domain_id	d1xdqb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

Domain ID domain_id	d1xdqc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

Domain ID domain_id	d1xdqd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

Domain ID domain_id	d1xdqe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamily	d.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family family	d.176.1.1 — Oxidoreductase molybdopterin-binding domain

CATH v4.4 (5 domains)

Domain ID domain_id	1xdqA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

Domain ID domain_id	1xdqB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

Domain ID domain_id	1xdqC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

Domain ID domain_id	1xdqD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

Domain ID domain_id	1xdqE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Oxidoreductase, molybdopterin-binding domain

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Unit-cell length a length_a	110.345 Å
Unit-cell length b length_b	165.064 Å
Unit-cell length c length_c	181.447 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	40

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	39.750 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2740

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase

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

Bacterial Sulfite Oxidase

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

1xdq__assembly_1__model_1

1xdq__assembly_1__model_1 | I(q)

1xdq__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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase

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

Bacterial Sulfite Oxidase

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

1xdq__assembly_1__model_1

1xdq__assembly_1__model_1 | I(q)

1xdq__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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)