SAXSdb — 1z5y

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

Thiol:disulfide interchange protein dsbD

Escherichia coli

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 dsbE × 1 （P0AA86） CHLORIDE ION × 3 1,2-ETHANEDIOL × 4 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
Chains and sequence ranges	Author chain D； PDBConstruct 1–143； UniProt 20–162

Thiol:disulfide interchange protein dsbE

Escherichia coli

UniProt P0AA86

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 dsbD × 1 （P36655） CHLORIDE ION × 3 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DSBE_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–143； UniProt 43–185

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	1z5y
Deposition date deposition_date	2005-03-21
Structure title title	Crystal Structure Of The Disulfide-Linked Complex Between The N-Terminal Domain Of The Electron Transfer Catalyst DsbD and The Cytochrome c Biogenesis Protein CcmG
Keywords keywords	DSBD, N-TERMINAL DOMAIN, IMMUNOGLOBULIN-LIKE, CCMG, THIOREDOXIN-LIKE, DISULFIDE-LINKED, OXIDOREDUCTASE-BIOSYNTHETIC PROTEIN COMPLEX; OXIDOREDUCTASE/BIOSYNTHETIC 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.

1z5y__assembly_1__model_1

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

Download this curve (.dat)

1z5y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z5y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.05 Å
Rg (electron density)	21.22 Å
Total Rg	22.14 Å
Atom count	2060
Residues	254
Excluded volume	36468 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z5y__assembly_1__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	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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	2426

GLFDAPGRSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGSADAGFCYPPETKTVPLSEVVANNAAPQPVSVPQQEQPTAQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Thiol:disulfide interchange protein dsbE
Molecular weight formula_weight	17084.3 kDa
Mutation mutation	C83S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

KPVPKFRLESLDNPGQFYQADVLTQGKPVLLNVWATWCPTSRAEHQYLNQLSAQGIRVVGMNYKDDRQKAISWLKELGNPYALSLFDGDGMLGLDLGVYGAPETFLIDGNGIIRYRHAGDLNPRVWEEEIKPLWEKYSKEAAQHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	253

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1z5yd_
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	d1z5ye1
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 (2 domains)

Domain ID domain_id	1z5yD00
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	1z5yE00
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	53.574 Å
Unit-cell length b length_b	53.165 Å
Unit-cell length c length_c	63.833 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2350
R_free r_free	0.2700

Crystal Structure Of The Disulfide-Linked Complex Between The N-Terminal Domain Of The Electron Transfer Catalyst DsbD and The Cytochrome c Biogenesis Protein CcmG

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

Thiol:disulfide interchange protein dsbE

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

1z5y__assembly_1__model_1

1z5y__assembly_1__model_1 | I(q)

1z5y__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure Of The Disulfide-Linked Complex Between The N-Terminal Domain Of The Electron Transfer Catalyst DsbD and The Cytochrome c Biogenesis Protein CcmG

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

Thiol:disulfide interchange protein dsbE

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

1z5y__assembly_1__model_1

1z5y__assembly_1__model_1 | I(q)

1z5y__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)