SAXSdb — 1t7d

▼

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	ARYLOMYCIN A2 × 1 10-METHYLUNDECANOIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	ARYLOMYCIN A2 × 1 10-METHYLUNDECANOIC ACID × 1 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1t7d
Deposition date deposition_date	2004-05-09
Structure title title	Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor
Keywords keywords	SIGNAL PEPTIDASE, SER/LYS DYAD, HYDROLASE, LIPOPEPTIDE, ANTIBIOTIC, BIARYL BRIDGE, HYDROLASE-ANTIBIOTIC COMPLEX; HYDROLASE/ANTIBIOTIC
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1t7d__assembly_1__model_1

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

Download this curve (.dat)

1t7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.36 Å
Rg (electron density)	17.34 Å
Total Rg	18.38 Å
Atom count	1804
Residues	226
Excluded volume	32053 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t7d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1t7d__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

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	3766

MIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQEGEWPTGLRLSRIGGIH

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	ARYLOMYCIN A2
Molecular weight formula_weight	644.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SAGGAY

Entity 3 Entity 3 non-polymer

Description description	10-METHYLUNDECANOIC ACID
Molecular weight formula_weight	200.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	265

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1t7da_
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	d1t7db_
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	1t7dA01
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	1t7dA02
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	1t7dB01
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	1t7dB02
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 —

▶

Unit-cell length a length_a	69.609 Å
Unit-cell length b length_b	69.609 Å
Unit-cell length c length_c	258.466 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	2.470 Å
Low-resolution limit resolution_low	29.540 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2830

Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor

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

1t7d__assembly_1__model_1

1t7d__assembly_1__model_1 | I(q)

1t7d__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (3)

Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor

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

1t7d__assembly_1__model_1

1t7d__assembly_1__model_1 | I(q)

1t7d__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (3)