3u41

Crystal structure of Escherichia coli DmsD in space group P212121

Method: X-RAY DIFFRACTION

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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	GLYCEROL × 6 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GLYCEROL × 5 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	GLYCEROL × 8 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GLYCEROL × 9 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	GLYCEROL × 8 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	GLYCEROL × 5 CHLORIDE ION × 2 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	GLYCEROL × 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 4–207； UniProt 1–204 Author chain B； PDBConstruct 4–207； UniProt 1–204 Author chain C； PDBConstruct 4–207； UniProt 1–204 Author chain D； PDBConstruct 4–207； UniProt 1–204 Author chain E； PDBConstruct 4–207； UniProt 1–204 Author chain F； PDBConstruct 4–207； UniProt 1–204 Author chain G； PDBConstruct 4–207； UniProt 1–204 Author chain H； PDBConstruct 4–207； 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	3u41
Deposition date deposition_date	2011-10-06
Structure title title	Crystal structure of Escherichia coli DmsD in space group P212121
Keywords keywords	TorD-like DmsD, Chaperone Translocation TorD-like TAT, preDmsA, Cytosol, CHAPERONE; 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.

3u41__assembly_1__model_1

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

Download this curve (.dat)

3u41__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u41__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.05 Å
Rg (electron density)	16.51 Å
Total Rg	17.73 Å
Atom count	1692
Residues	204
Excluded volume	30183 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u41__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3u41__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3u41__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3u41__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3u41__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3u41__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3u41__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3u41__assembly_8__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 (7)

Entity 1 Entity 1 polymer

Description description	Twin-arginine leader-binding protein dmsD
Molecular weight formula_weight	23645.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	13942

GSHMTHFSQQDNFSVAARVLGALFYYAPESAEAAPLVAVLTSDGWETQWPLPEASLAPLVTAFQTQCEETHAQAWQRLFVGPWALPSPPWGSVWLDRESVLFGDSTLALRQWMREKGIQFEMKQNEPEDHFGSLLLMAAWLAENGRQTECEELLAWHLFPWSTRFLDVFIEKAEHPFYRALGELARLTLAQWQSQLLIPVAVKPLFR

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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	42

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 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	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	458

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3u41a_
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	d3u41b_
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	d3u41c_
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	d3u41d_
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	d3u41e_
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	d3u41f_
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	d3u41g_
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	d3u41h_
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

CATH v4.4 (8 domains)

Domain ID domain_id	3u41A00
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	3u41B00
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	3u41C00
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	3u41D00
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	3u41E00
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	3u41F00
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	3u41G00
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	3u41H00
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	94.275 Å
Unit-cell length b length_b	96.221 Å
Unit-cell length c length_c	210.243 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	48.600 Å
R factor r_factor	0.2319
R_work r_work	0.2298
R_free r_free	0.2707

Crystal structure of Escherichia coli DmsD in space group P212121

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

3u41__assembly_1__model_1

3u41__assembly_1__model_1 | I(q)

3u41__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (0)

Crystal structure of Escherichia coli DmsD in space group P212121

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

3u41__assembly_1__model_1

3u41__assembly_1__model_1 | I(q)

3u41__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (0)