SAXSdb — 3s04

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

Signal peptidase I

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	Glyco-Arylomycin × 1 14-methylhexadec-9-enoic acid × 1 alpha-L-rhamnopyranose × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Glyco-Arylomycin × 1 14-methylhexadec-9-enoic acid × 1 alpha-L-rhamnopyranose × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Glyco-Arylomycin × 2 14-methylhexadec-9-enoic acid × 2 alpha-L-rhamnopyranose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LEP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–250； UniProt 76–324 Author chain B； PDBConstruct 2–250； UniProt 76–324

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	3s04
Deposition date deposition_date	2011-05-13
Structure title title	Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic
Keywords keywords	;mostly-beta fold, Membrane bound, serine protease, Secreted preproteins, Cytoplasmic membrane, HYDROLASE-ANTIBIOTIC complex, signal peptidase, leader peptidase, signal peptide, leader peptide, serine-lysine dyad ;; HYDROLASE/ANTIBIOTIC
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.

3s04__assembly_1__model_1

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

Download this curve (.dat)

3s04__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3s04__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)	16.97 Å
Total Rg	18.09 Å
Atom count	1708
Residues	212
Excluded volume	30371 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3s04__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3s04__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3s04__assembly_3__model_1`	tetrameric （4）	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	Signal peptidase I
Molecular weight formula_weight	28079.8 kDa
EC 编号 ec_number	3.4.21.89
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	3613

MIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH

Source Source

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

Entity 2 Entity 2 polymer

Description description	Glyco-Arylomycin
Molecular weight formula_weight	660.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J

SAGXAY

Entity 3 Entity 3 non-polymer

Description description	14-methylhexadec-9-enoic acid
Molecular weight formula_weight	268.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	alpha-L-rhamnopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3s04a_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.2 — Type 1 signal peptidase

Domain ID domain_id	d3s04b_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.2 — Type 1 signal peptidase

CATH v4.4 (4 domains)

Domain ID domain_id	3s04A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	3s04A02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	230 — Signal Peptidase I; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3s04B01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	3s04B02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	230 — Signal Peptidase I; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	72.010 Å
Unit-cell length b length_b	72.010 Å
Unit-cell length c length_c	262.570 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.440 Å
Low-resolution limit resolution_low	32.200 Å
R factor r_factor	0.2460
R_work r_work	0.2451
R_free r_free	0.2647

Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic

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

Signal peptidase I

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

3s04__assembly_1__model_1

3s04__assembly_1__model_1 | I(q)

3s04__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic

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

Signal peptidase I

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

3s04__assembly_1__model_1

3s04__assembly_1__model_1 | I(q)

3s04__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)