2c1d

Crystal structure of SoxXA from P. pantotrophus

Method: X-RAY DIFFRACTION

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

SOXA

PARACOCCUS DENITRIFICANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SOXX × 1 （Q9LCV0） HEME C × 3 ZINC ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SOXX × 1 （Q9LCV0） HEME C × 3 ZINC ION × 3 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	SOXX × 1 （Q9LCV0） HEME C × 3 ZINC ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	SOXX × 1 （Q9LCV0） HEME C × 3 ZINC ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O33434_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 27–290 Author chain C； PDBConstruct 1–264； UniProt 27–290 Author chain E； PDBConstruct 1–264； UniProt 27–290 Author chain G； PDBConstruct 1–264； UniProt 27–290

SOXX

PARACOCCUS PANTOTROPHUS

UniProt Q9LCV0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SOXA × 1 （O33434） HEME C × 3 ZINC ION × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SOXA × 1 （O33434） HEME C × 3 ZINC ION × 3 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	SOXA × 1 （O33434） HEME C × 3 ZINC ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	SOXA × 1 （O33434） HEME C × 3 ZINC ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LCV0_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–137； UniProt 21–157 Author chain D； PDBConstruct 1–137； UniProt 21–157 Author chain F； PDBConstruct 1–137； UniProt 21–157 Author chain H； PDBConstruct 1–137； UniProt 21–157

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	2c1d
Deposition date deposition_date	2005-09-13
Structure title title	Crystal structure of SoxXA from P. pantotrophus
Keywords keywords	SULFUR OXIDATION, CYTOCHROME-C-TYPE, 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.

2c1d__assembly_1__model_1

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

Download this curve (.dat)

2c1d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c1d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.47 Å
Rg (electron density)	23.77 Å
Total Rg	24.60 Å
Atom count	3182
Residues	400
Excluded volume	56238 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c1d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2c1d__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2c1d__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2c1d__assembly_4__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	SOXA
Molecular weight formula_weight	29281.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	14878

DPVEDGLVIETDSGPVEIVTKTAPPAFLADTFDTIYSGWHFRDDSTRDLERDDFDNPAMVFVDRGLDKWNAAMGVNGESCASCHQGPESMAGLRAVMPRVDEHTGKLMIMEDYVNACVTERMGLEKWGVTSDNMKDMLSLISLQSRGMAVNVKIDGPAAPYWEHGKEIYYTRYGQLEMSCANCHEDNAGNMIRADHLSQGQINGFPTYRLKDSGMVTAQHRFVGCVRDTRAETFKAGSDDFKALELYVASRGNGLSVEGVSVRH

Source Source

Source organism organism	PARACOCCUS DENITRIFICANS
NCBI taxonomy ID ncbi_taxonomy_id	266
Host organism host_organism	PARACOCCUS PANTOTROPHUS

Entity 2 Entity 2 polymer

Description description	SOXX
Molecular weight formula_weight	14330.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

CETAPKEVVYVEGAVEASLTGAPGNPEEGVRIMTTNALGNCVACHQIGALPDVEFPGTIAPPLDGAGDRWTEAQLRGIVANAKMTFEGTFMPAFYKVDGFVRPGDGFSGKAGAEPLAPILNAQQIEDVVAFLVTLKE

Source Source

Source organism organism	PARACOCCUS PANTOTROPHUS
NCBI taxonomy ID ncbi_taxonomy_id	82367
Host organism host_organism	PARACOCCUS PANTOTROPHUS

Entity 3 Entity 3 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2151

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2c1da1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1da2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1db_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1dc1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1dc2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1dd_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1de1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1de2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1df_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1dg1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1dg2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d2c1dh_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	2c1dA01
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	2c1dA02
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	2c1dB00
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	2c1dC01
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	2c1dC02
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	2c1dD00
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	2c1dE01
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	2c1dE02
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	2c1dF00
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	2c1dG01
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	2c1dG02
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	2c1dH00
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

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Unit-cell length a length_a	42.860 Å
Unit-cell length b length_b	180.010 Å
Unit-cell length c length_c	117.930 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.83 °
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	1.920 Å
Low-resolution limit resolution_low	119.520 Å
R factor r_factor	0.1610
R_work r_work	0.1590
R_free r_free	0.2110

Crystal structure of SoxXA from P. pantotrophus

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

SOXA

State in the Current Structure

Other States of the Same Protein in the Database

SOXX

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

2c1d__assembly_1__model_1

2c1d__assembly_1__model_1 | I(q)

2c1d__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of SoxXA from P. pantotrophus

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

SOXA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SOXX

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

2c1d__assembly_1__model_1

2c1d__assembly_1__model_1 | I(q)

2c1d__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)