2xts

Crystal Structure of the Sulfane Dehydrogenase SoxCD from Paracoccus pantotrophus

Method: X-RAY DIFFRACTION

▼

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

SULFITE DEHYDROGENASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CYTOCHROME × 2 （O07819） 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 × 2 MOLYBDENUM (IV)OXIDE × 2 COBALT (II) ION × 2 GLYCEROL × 9 HEME C × 2 CALCIUM ION × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P72178_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–390； UniProt 41–430 Author chain C； PDBConstruct 1–390； UniProt 41–430

CYTOCHROME

OrganismNot specified

UniProt O07819

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	SULFITE DEHYDROGENASE × 2 （P72178） 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 × 2 MOLYBDENUM (IV)OXIDE × 2 COBALT (II) ION × 2 GLYCEROL × 9 HEME C × 2 CALCIUM ION × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O07819_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–205； UniProt 1–205 Author chain D； PDBConstruct 1–205； UniProt 1–205

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2xts
Deposition date deposition_date	2010-10-12
Structure title title	Crystal Structure of the Sulfane Dehydrogenase SoxCD from Paracoccus pantotrophus
Keywords keywords	OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX, SOX SYSTEM, SULFANE OXIDATION, MOLYBDENUM COFACTOR, HEME, ELECTRON TRANSFER; OXIDOREDUCTASE/ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2xts__assembly_1__model_1

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

Download this curve (.dat)

2xts__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xts__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.13 Å
Rg (electron density)	32.71 Å
Total Rg	33.16 Å
Atom count	9375
Residues	1186
Excluded volume	165560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xts__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	SULFITE DEHYDROGENASE
Molecular weight formula_weight	43494.1 kDa
EC 编号 ec_number	1.8.2.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	10441

AGTPDPLITEIQPWASEFGEAVDAHPYGLPIHFESHVKRQYVEWLTESPVSSINFTPIHALEGTITPQGCAFERHHSGAIELSKQDYRLMINGLVEKPLVFTFEDLLRFPRTTTTAFCECAANGGMEWGGAQLEGCQYTQGMIHNMEYVGVPLSVLLAEAGVKPEGKWLYAEGADASSNGRSFPMEKVMDDVMLAFFANGEALRKEHGYPARLVVPGWEGNMWVKWVRRLGIYDKAVESREETSKYTDLMPDGRARKWTWVMDAKSVITSPSPQVPIRHGKGPLVISGLAWSGNGRITRVDVSLDGGKNWTTARITGQALPKALTRFHLDIDWDGSEMLLQSRAVDETGYVQPTKDALRAIRGRNNVYHNNGIQTWWVKADGEVENVEIA

Entity 2 Entity 2 polymer

Description description	CYTOCHROME
Molecular weight formula_weight	21898.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

DKLGLGREALPEEISAWDTAVLPDGQGLRPGSGDVATGDALFADNCASCHGDFAEGLDSWPVLAGGDGSLTDPRPVKTIGSYWPYLSTVYDYVHRSMPFGSAQTLSVDDTYAITAFLLYSNGLVEDDFVLTHENFTQVVLPNAEGFYPDDRDQTEYPLFSKEPCMTDCAVGVEITKRAVDLNVTPEDPDGRPAGSMPDLGAAAAP

Entity 3 Entity 3 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	2

Entity 4 Entity 4 non-polymer

Description description	MOLYBDENUM (IV)OXIDE
Molecular weight formula_weight	127.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 7 Entity 7 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	956

▼

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2xtsA01
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	2xtsA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	650 —

Domain ID domain_id	2xtsB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2xtsC01
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	2xtsC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	650 —

Domain ID domain_id	2xtsD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

▶

Unit-cell length a length_a	122.970 Å
Unit-cell length b length_b	122.970 Å
Unit-cell length c length_c	76.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.330 Å
Low-resolution limit resolution_low	50.010 Å
R factor r_factor	0.1070
R_work r_work	0.1070
R_free r_free	0.1111

Crystal Structure of the Sulfane Dehydrogenase SoxCD from Paracoccus pantotrophus

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

SULFITE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

CYTOCHROME

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

2xts__assembly_1__model_1

2xts__assembly_1__model_1 | I(q)

2xts__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of the Sulfane Dehydrogenase SoxCD from Paracoccus pantotrophus

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

SULFITE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CYTOCHROME

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

2xts__assembly_1__model_1

2xts__assembly_1__model_1 | I(q)

2xts__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)