SAXSdb — 6a4r

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

Peptidase E

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ASPARTIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEPE_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 38–265； UniProt 2–229 Author chain B； PDBConstruct 38–265； UniProt 2–229

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	6a4r
Deposition date deposition_date	2018-06-20
Structure title title	Crystal structure of aspartate bound peptidase E from Salmonella enterica
Keywords keywords	S51 peptidase, peptidase E, dimer, active site, active site loop, HYDROLASE; 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.

6a4r__assembly_1__model_1

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

Download this curve (.dat)

6a4r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6a4r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.11 Å
Rg (electron density)	23.22 Å
Total Rg	24.10 Å
Atom count	3550
Residues	465
Excluded volume	63126 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6a4r__assembly_1__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Peptidase E
Molecular weight formula_weight	28596.2 kDa
EC 编号 ec_number	3.4.13.21
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	3846

MASWSHPQFEKGSSHHHHHHSSGSGGGGGENLYFQGSELLLLSNSTLPGKAWLEHALPLIANQLNGRRSAVFIPFAGVTQTWDEYTDKTAEVLAPLGVNVTGIHRVADPLAAIEKAEIIIVGGGNTFQLLKESRERGLLAPMADRVKRGALYIGWSAGANLACPTIRTTNDMPIVDPNGFDALDLFPLQINPHFTNALPEGHKGETREQRIRELLVVAPELTVIGLPEGNWIQVSNGQAVLGGPNTTWVFKAGEEAVALEAGHRF

Source Source

Source organism organism	Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
NCBI taxonomy ID ncbi_taxonomy_id	99287
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ASPARTIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	269

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6a4ra1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.4 — Aspartyl dipeptidase PepE

Domain ID domain_id	d6a4ra2
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

Domain ID domain_id	d6a4rb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.4 — Aspartyl dipeptidase PepE

Domain ID domain_id	d6a4rb2
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	6a4rA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

Domain ID domain_id	6a4rB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

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Unit-cell length a length_a	67.155 Å
Unit-cell length b length_b	42.889 Å
Unit-cell length c length_c	89.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.828 Å
Low-resolution limit resolution_low	41.605 Å
R factor r_factor	0.1902
R_work r_work	0.1890
R_free r_free	0.2126

Crystal structure of aspartate bound peptidase E from Salmonella enterica

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

Peptidase E

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

6a4r__assembly_1__model_1

6a4r__assembly_1__model_1 | I(q)

6a4r__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of aspartate bound peptidase E from Salmonella enterica

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

Peptidase E

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

6a4r__assembly_1__model_1

6a4r__assembly_1__model_1 | I(q)

6a4r__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)