SAXSdb — 3giu

▼

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

Pyrrolidone-carboxylate peptidase

Staphylococcus aureus subsp. aureus COL

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 ACETIC ACID × 2 TETRAETHYLENE GLYCOL × 3 GLYCEROL × 2 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCP_STAAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–215； UniProt 1–212 Author chain B； PDBConstruct 4–215； UniProt 1–212

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	3giu
Deposition date deposition_date	2009-03-06
Structure title title	1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus
Keywords keywords	;pyrrolidone-carboxylate peptidase, idp00836, Hydrolase, Protease, Thiol protease, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID ;; HYDROLASE
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.

3giu__assembly_1__model_1

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

Download this curve (.dat)

3giu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3giu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.27 Å
Rg (electron density)	21.42 Å
Total Rg	22.23 Å
Atom count	3345
Residues	419
Excluded volume	59738 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3giu__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Pyrrolidone-carboxylate peptidase
Molecular weight formula_weight	23603.1 kDa
EC 编号 ec_number	3.4.19.3
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	4362

SNAMHILVTGFAPFDNQNINPSWEAVTQLEDIIGTHTIDKLKLPTSFKKVDNIINKTLASNHYDVVLAIGQAGGRNAITPERVAINIDDARIPDNDDFQPIDQAIHLDGAPAYFSNLPVKAMTQSIINQGLPGALSNSAGTFVCNHTLYHLGYLQDKHYPHLRFGFIHVPYIPEQVIGKPDTPSMPLEKIVAGLTAAIEAISNDEDLHLALGTTE

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus COL
NCBI taxonomy ID ncbi_taxonomy_id	93062
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	619

▼

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3giua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.4 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
Family Family family	c.56.4.0 — automated matches

Domain ID domain_id	d3giub1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.4 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
Family Family family	c.56.4.0 — automated matches

Domain ID domain_id	d3giub2
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	3giuA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	20 — Peptidase C15, pyroglutamyl peptidase I-like

Domain ID domain_id	3giuB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	20 — Peptidase C15, pyroglutamyl peptidase I-like

▶

Unit-cell length a length_a	42.790 Å
Unit-cell length b length_b	81.000 Å
Unit-cell length c length_c	119.910 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	8

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

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	24.550 Å
R factor r_factor	0.1177
R_work r_work	0.1162
R_free r_free	0.1478

1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus

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

Pyrrolidone-carboxylate peptidase

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

3giu__assembly_1__model_1

3giu__assembly_1__model_1 | I(q)

3giu__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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus

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

Pyrrolidone-carboxylate peptidase

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

3giu__assembly_1__model_1

3giu__assembly_1__model_1 | I(q)

3giu__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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)