SAXSdb — 3efp

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

Twin-arginine leader-binding protein dmsD

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 GLYCEROL × 4 CHLORIDE ION × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 GLYCEROL × 2 CHLORIDE ION × 3 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DMSD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–208； UniProt 1–204 Author chain B； PDBConstruct 5–208； UniProt 1–204

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	3efp
Deposition date deposition_date	2008-09-09
Structure title title	Crystal structure of the Escherichia coli twin arginine leader peptide binding protein DmsD in a monomeric form
Keywords keywords	;twin-arginine translocation (Tat), protein targeting, protein translocation, chaperone, leader peptide, signal peptide, redox enzyme maturation protein (REMP) ;; CHAPERONE
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.

3efp__assembly_2__model_1

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

Download this curve (.dat)

3efp__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3efp__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.51 Å
Rg (electron density)	17.03 Å
Total Rg	18.20 Å
Atom count	1722
Residues	208
Excluded volume	30723 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3efp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3efp__assembly_2__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	Twin-arginine leader-binding protein dmsD
Molecular weight formula_weight	23851.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3860

RWGSMTHFSQQDNFSVAARVLGALFYYAPESAEAAPLVAVLTSDGWETQWPLPEASLAPLVTAFQTQCEETHAQAWQRLFVGPWALPSPPWGSVWLDRESVLFGDSTLALRQWMREKGIQFEMKQNEPEDHFGSLLLMAAWLAENGRQTECEELLAWHLFPWSTRFLDVFIEKAEHPFYRALGELARLTLAQWQSQLLIPVAVKPLFR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	411

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3efpa_
Class class	a — All alpha proteins
Fold Fold fold	a.184 — TorD-like
Superfamily Superfamily superfamily	a.184.1 — TorD-like
Family Family family	a.184.1.1 — TorD-like

Domain ID domain_id	d3efpb1
Class class	a — All alpha proteins
Fold Fold fold	a.184 — TorD-like
Superfamily Superfamily superfamily	a.184.1 — TorD-like
Family Family family	a.184.1.1 — TorD-like

Domain ID domain_id	d3efpb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3efpA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3480 — TorD-like
Homologous superfamily homologous superfamily	10 — TorD-like

Domain ID domain_id	3efpB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3480 — TorD-like
Homologous superfamily homologous superfamily	10 — TorD-like

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Unit-cell length a length_a	128.020 Å
Unit-cell length b length_b	128.020 Å
Unit-cell length c length_c	78.723 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	30.750 Å
R factor r_factor	0.1800
R_work r_work	0.1780
R_free r_free	0.2130

Crystal structure of the Escherichia coli twin arginine leader peptide binding protein DmsD in a monomeric form

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

Twin-arginine leader-binding protein dmsD

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

3efp__assembly_2__model_1

3efp__assembly_2__model_1 | I(q)

3efp__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the Escherichia coli twin arginine leader peptide binding protein DmsD in a monomeric form

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

Twin-arginine leader-binding protein dmsD

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

3efp__assembly_2__model_1

3efp__assembly_2__model_1 | I(q)

3efp__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)