SAXSdb — 4txv

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

Thiol:disulfide interchange protein TlpA

Bradyrhizobium diazoefficiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cytochrome c oxidase subunit 2 × 1 （H7C6E5） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cytochrome c oxidase subunit 2 × 1 （H7C6E5） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TLPA_BRADU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–184； UniProt 38–221 Author chain C； PDBConstruct 1–184； UniProt 38–221

Cytochrome c oxidase subunit 2

Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)

UniProt H7C6E5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Thiol:disulfide interchange protein TlpA × 1 （P43221） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Thiol:disulfide interchange protein TlpA × 1 （P43221） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H7C6E5_BRADU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–159； UniProt 123–279 Author chain D； PDBConstruct 3–159； UniProt 123–279

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	4txv
Deposition date deposition_date	2014-07-07
Structure title title	Crystal structure of the mixed disulfide intermediate between thioredoxin-like TlpAs(C110S) and subunit II of cytochrome c oxidase CoxBPD (C233S)
Keywords keywords	thioredoxin, mixed disulphide, cytochrome c oxidase, protein binding; PROTEIN BINDING
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.

4txv__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4txv__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4txv__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.18 Å
Rg (electron density)	20.10 Å
Total Rg	21.06 Å
Atom count	2382
Residues	311
Excluded volume	42895 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4txv__assembly_1__model_1`	Dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4txv__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Thiol:disulfide interchange protein TlpA
Molecular weight formula_weight	19528.6 kDa
Mutation mutation	C110S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5267

APTGDPACRAAVATAQKIAPLAHGEVAALTMASAPLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPSRKEMPALDELQGKLSGPNFEVVAINIDTRDPEKPKTFLKEANLTRLGYFNDQKAKVFQDLKAIGRALGMPTSVLVDPQGCEIATIAGPAEWASEDALKLIRAATGKAAAAL

Source Source

Source organism organism	Bradyrhizobium diazoefficiens
NCBI taxonomy ID ncbi_taxonomy_id	224911
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	17416.9 kDa
EC 编号 ec_number	1.9.3.1
Mutation mutation	C233S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAFLELDVPKADLTIKATGKQWYWSYAYPDNGKFEFDSLMAQDKQPRLLGVDNEMVVPVNKVIRVQVTGADVIHAFALPAFGVKIDAIPGRLNETWFKAAKTGMFYGQCSELSGKDHAFMPIAIRVVEDKEFASWVETAKKKFASGGTGTYASAAGPTQ

Source Source

Source organism organism	Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
NCBI taxonomy ID ncbi_taxonomy_id	224911
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	444

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4txva_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d4txvc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.10 — Glutathione peroxidase-like

CATH v4.4 (4 domains)

Domain ID domain_id	4txvA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	4txvB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	4txvC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	4txvD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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Unit-cell length a length_a	74.830 Å
Unit-cell length b length_b	81.640 Å
Unit-cell length c length_c	109.370 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	65.420 Å
R factor r_factor	0.1654
R_work r_work	0.1629
R_free r_free	0.2116

Crystal structure of the mixed disulfide intermediate between thioredoxin-like TlpAs(C110S) and subunit II of cytochrome c oxidase CoxBPD (C233S)

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

Thiol:disulfide interchange protein TlpA

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome c oxidase subunit 2

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

4txv__assembly_2__model_1

4txv__assembly_2__model_1 | I(q)

4txv__assembly_2__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the mixed disulfide intermediate between thioredoxin-like TlpAs(C110S) and subunit II of cytochrome c oxidase CoxBPD (C233S)

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

Thiol:disulfide interchange protein TlpA

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 c oxidase subunit 2

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

4txv__assembly_2__model_1

4txv__assembly_2__model_1 | I(q)

4txv__assembly_2__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)