SAXSdb — 3rnz

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

Pyrrolidone-carboxylate peptidase

Bacillus amyloliquefaciens

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	PCP_BACAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–215； UniProt 1–215 Author chain B； PDBConstruct 1–215； UniProt 1–215 Author chain C； PDBConstruct 1–215； UniProt 1–215 Author chain D； PDBConstruct 1–215； UniProt 1–215

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	3rnz
Deposition date deposition_date	2011-04-24
Structure title title	Crystal structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I
Keywords keywords	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.

3rnz__assembly_1__model_1

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

Download this curve (.dat)

3rnz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rnz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.37 Å
Rg (electron density)	29.25 Å
Total Rg	29.97 Å
Atom count	6337
Residues	828
Excluded volume	112960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rnz__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)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3rnza_
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.56.4.1 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)

Domain ID domain_id	d3rnzb_
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.56.4.1 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)

Domain ID domain_id	d3rnzc_
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.56.4.1 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)

Domain ID domain_id	d3rnzd_
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.56.4.1 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)

CATH v4.4 (4 domains)

Domain ID domain_id	3rnzA00
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	3rnzB00
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	3rnzC00
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	3rnzD00
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

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Unit-cell length a length_a	289.890 Å
Unit-cell length b length_b	45.360 Å
Unit-cell length c length_c	68.090 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1760
R_work r_work	0.1740
R_free r_free	0.2090

Description description	Pyrrolidone-carboxylate peptidase
Molecular weight formula_weight	24376.7 kDa
EC 编号 ec_number	3.4.19.3
Mutation mutation	M58I, A202V
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6774

Crystal structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I

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

3rnz__assembly_1__model_1

3rnz__assembly_1__model_1 | I(q)

3rnz__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Bacillus amyloliquefaciens
NCBI taxonomy ID ncbi_taxonomy_id	1390
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	437

Crystal structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I

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

3rnz__assembly_1__model_1

3rnz__assembly_1__model_1 | I(q)

3rnz__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)