1vrs

Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD

Method: X-RAY DIFFRACTION

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

Thiol:disulfide interchange protein dsbD

Escherichia coli str. K12 substr.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DSBD_ECOLI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–143； UniProt 20–162 Author chain B； PDBConstruct 1–143； UniProt 20–162 Author chain C； PDBConstruct 1–143； UniProt 20–162 Author chain D； PDBConstruct 1–128； UniProt 438–565 Author chain E； PDBConstruct 1–128； UniProt 438–565 Author chain F； PDBConstruct 1–128； UniProt 438–565

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	1vrs
Deposition date deposition_date	2005-06-17
Structure title title	Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD
Keywords keywords	DsbD, immunoglobulin-like, thioredoxin-like, disulfide-linked, 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.

1vrs__assembly_1__model_1

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

Download this curve (.dat)

1vrs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vrs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.97 Å
Rg (electron density)	21.12 Å
Total Rg	21.92 Å
Atom count	1901
Residues	239
Excluded volume	33663 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vrs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vrs__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1vrs__assembly_3__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 dsbD
Molecular weight formula_weight	15982.6 kDa
EC 编号 ec_number	1.8.1.8
Mutation mutation	C103S
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5954

GLFDAPGRSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGSADAGFCYPPETKTVPLSEVVANNAAPQPVSVPQQEQPTAQ

Source Source

Source organism organism	Escherichia coli str. K12 substr.
NCBI taxonomy ID ncbi_taxonomy_id	316407
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Thiol:disulfide interchange protein dsbD
Molecular weight formula_weight	15081.9 kDa
EC 编号 ec_number	1.8.1.8
Mutation mutation	C464S
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

ATHTAQTQTHLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVASKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQPHHHHHH

Source Source

Source organism organism	Escherichia coli str. K12 substr.
NCBI taxonomy ID ncbi_taxonomy_id	316407
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	284

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1vrsa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.17 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)
Family Family family	b.1.17.1 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)

Domain ID domain_id	d1vrsb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.17 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)
Family Family family	b.1.17.1 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)

Domain ID domain_id	d1vrsc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.17 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)
Family Family family	b.1.17.1 — Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)

Domain ID domain_id	d1vrsd_
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.47.1.1 — Thioltransferase

Domain ID domain_id	d1vrse_
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.47.1.1 — Thioltransferase

Domain ID domain_id	d1vrsf_
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.47.1.1 — Thioltransferase

CATH v4.4 (6 domains)

Domain ID domain_id	1vrsA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1250 — Thiol:disulfide interchange protein DsbD, N-terminal domain

Domain ID domain_id	1vrsB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1250 — Thiol:disulfide interchange protein DsbD, N-terminal domain

Domain ID domain_id	1vrsC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1250 — Thiol:disulfide interchange protein DsbD, N-terminal domain

Domain ID domain_id	1vrsD00
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	1vrsE00
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	1vrsF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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Unit-cell length a length_a	188.460 Å
Unit-cell length b length_b	52.600 Å
Unit-cell length c length_c	107.920 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2240
R_free r_free	0.2840

Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD

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

Thiol:disulfide interchange protein dsbD

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

1vrs__assembly_1__model_1

1vrs__assembly_1__model_1 | I(q)

1vrs__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 (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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD

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

Thiol:disulfide interchange protein dsbD

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

1vrs__assembly_1__model_1

1vrs__assembly_1__model_1 | I(q)

1vrs__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 (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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)