3bez

Crystal structure of Escherichia coli Signal peptide peptidase (SppA), SeMet crystals

Method: X-RAY DIFFRACTION

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

Protease 4

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–593； UniProt 47–618 Author chain B； PDBConstruct 22–593； UniProt 47–618 Author chain C； PDBConstruct 22–593； UniProt 47–618 Author chain D； PDBConstruct 22–593； UniProt 47–618

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	3bez
Deposition date deposition_date	2007-11-20
Structure title title	Crystal structure of Escherichia coli Signal peptide peptidase (SppA), SeMet crystals
Keywords keywords	protease, bacterial, Hydrolase, Inner membrane, Membrane, Transmembrane; HYDROLASE
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.

3bez__assembly_1__model_1

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

Download this curve (.dat)

3bez__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bez__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.01 Å
Rg (electron density)	43.29 Å
Total Rg	43.62 Å
Atom count	14362
Residues	1869
Excluded volume	255280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bez__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Description description	Protease 4
Molecular weight formula_weight	64623.1 kDa
EC 编号 ec_number	3.4.21.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14989

MGSSHHHHHHSSGLVPRGSHMGGDSKETASRGALLLDISGVIVDKPDSSQRFSKLSRQLLGASSDRLQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEYYVDEPTFFDKVMDNMSGSVRAMLPDAFQAMLPAPLASVASTVKSESDKLAAFNDPQNRYAFCLTCANMR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	627

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3bezA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3bezA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1750 — peptide peptidase (sppa) fold
Homologous superfamily homologous superfamily	10 — peptide peptidase (sppa) like domain

Domain ID domain_id	3bezA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3bezB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3bezB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1750 — peptide peptidase (sppa) fold
Homologous superfamily homologous superfamily	10 — peptide peptidase (sppa) like domain

Domain ID domain_id	3bezB03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3bezC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3bezC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1750 — peptide peptidase (sppa) fold
Homologous superfamily homologous superfamily	10 — peptide peptidase (sppa) like domain

Domain ID domain_id	3bezC03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3bezD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	3bezD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1750 — peptide peptidase (sppa) fold
Homologous superfamily homologous superfamily	10 — peptide peptidase (sppa) like domain

Domain ID domain_id	3bezD03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

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Unit-cell length a length_a	93.022 Å
Unit-cell length b length_b	153.040 Å
Unit-cell length c length_c	100.214 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.760 Å
Low-resolution limit resolution_low	46.630 Å
R factor r_factor	0.2030
R_work r_work	0.2000
R_free r_free	0.2590

Crystal structure of Escherichia coli Signal peptide peptidase (SppA), SeMet crystals

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

Protease 4

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

3bez__assembly_1__model_1

3bez__assembly_1__model_1 | I(q)

3bez__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of Escherichia coli Signal peptide peptidase (SppA), SeMet crystals

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

Protease 4

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

3bez__assembly_1__model_1

3bez__assembly_1__model_1 | I(q)

3bez__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)