SAXSdb — 2oxh

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

SoxZ protein

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	SoxY protein × 1 （Q9LCU9） 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SoxY protein × 1 （Q9LCU9） 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	SoxY protein × 1 （Q9LCU9） 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	SoxY protein × 1 （Q9LCU9） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LCU8_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–107； UniProt 2–108 Author chain C； PDBConstruct 1–107； UniProt 2–108 Author chain E； PDBConstruct 1–107； UniProt 2–108 Author chain Z； PDBConstruct 1–107； UniProt 2–108

SoxY protein

Paracoccus denitrificans

UniProt Q9LCU9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SoxZ protein × 1 （Q9LCU8） 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SoxZ protein × 1 （Q9LCU8） 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	SoxZ protein × 1 （Q9LCU8） 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	SoxZ protein × 1 （Q9LCU8） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LCU9_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 12–124； UniProt 28–140 Author chain D； PDBConstruct 12–124； UniProt 28–140 Author chain F； PDBConstruct 12–124； UniProt 28–140 Author chain Y； PDBConstruct 12–124； UniProt 28–140

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	2oxh
Deposition date deposition_date	2007-02-20
Structure title title	The SOXYZ Complex of Paracoccus Pantotrophus
Keywords keywords	IMMUNOGLOBULIN-LIKE BETA-SANDWICH FOLD, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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.

2oxh__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2oxh__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2oxh__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	18.53 Å
Rg (electron density)	17.35 Å
Total Rg	18.41 Å
Atom count	1597
Residues	220
Excluded volume	28359 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2oxh__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2oxh__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2oxh__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2oxh__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 (4)

Entity 1 Entity 1 polymer

Description description	SoxZ protein
Molecular weight formula_weight	11663.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z,A,C,E
Atom count atom_count	6822

ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAV

Source Source

Source organism organism	Paracoccus denitrificans
NCBI taxonomy ID ncbi_taxonomy_id	266
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	SoxY protein
Molecular weight formula_weight	12470.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MRGSHHHHHHGSSTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGCGG

Source Source

Source organism organism	Paracoccus denitrificans
NCBI taxonomy ID ncbi_taxonomy_id	266
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	395

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2oxha_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.0 — automated matches

Domain ID domain_id	d2oxhc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.0 — automated matches

Domain ID domain_id	d2oxhe_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.0 — automated matches

Domain ID domain_id	d2oxhz_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2oxhA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2oxhB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2470 — SoxY domain

Domain ID domain_id	2oxhC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2oxhD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2470 — SoxY domain

Domain ID domain_id	2oxhE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2oxhF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2470 — SoxY domain

Domain ID domain_id	2oxhY00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2470 — SoxY domain

Domain ID domain_id	2oxhZ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	40.220 Å
Unit-cell length b length_b	54.490 Å
Unit-cell length c length_c	104.872 Å
Unit-cell angle α angle_alpha	103.13 °
Unit-cell angle β angle_beta	95.21 °
Unit-cell angle γ angle_gamma	90.01 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1966
R_work r_work	0.1939
R_free r_free	0.2443

The SOXYZ Complex of Paracoccus Pantotrophus

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

SoxZ protein

State in the Current Structure

Other States of the Same Protein in the Database

SoxY 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

2oxh__assembly_4__model_1

2oxh__assembly_4__model_1 | I(q)

2oxh__assembly_4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

The SOXYZ Complex of Paracoccus Pantotrophus

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

SoxZ 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

SoxY 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

2oxh__assembly_4__model_1

2oxh__assembly_4__model_1 | I(q)

2oxh__assembly_4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)