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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–215 Chain B； UniProt 1–215 Chain C； UniProt 1–215 Chain D； UniProt 1–215	Mutation：M58I, A202V	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.9；298 K；1.8M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.01 Å R-free 0.209

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3RNZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AUG CRYSTAL STRUCTURE OF THE PYROGLUTAMYL PEPTIDASE I FROM BACILLUS AMYLOLIQUEFACIENS Deposited 1997-08-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–215（215 aa） Chain B 1–215（215 aa） Chain C 1–215（215 aa） Chain D 1–215（215 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.259
3RO0 Crystal structure of Bacillus amyloliquefaciens pyroglutamyl peptidase I and terpyridine platinum(II) Deposited 2011-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–215（215 aa） Chain B 1–215（215 aa） Chain C 1–215（215 aa） Chain D 1–215（215 aa）	Mutation：M58I, A202V Mutation：M58I, A202V Mutation：M58I, A202V Mutation：M58I, A202V	TPT 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；298 K；1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.50 Å R-free 0.205

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.37 Å
Radius of gyration Rg (electron density) rg_electron	29.25 Å
Forward intensity I(0) i0	126312000.00
Molecular weight molecular_weight	89863.0 kDa
Excluded volume excluded_volume	112960 Å³
Envelope volume envelope_volume	137760 Å³
Hydration-shell volume shell_volume	38910 Å³
Envelope diameter envelope_diameter	94.6 Å
Shell Rg shell_rg	37.04 Å
Envelope Rg envelope_rg	28.59 Å
Shape Rg shape_rg	29.25 Å
Total Rg total_rg	29.97 Å
Total atoms total_atoms	6337
Residues n_residues	828
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	94.2 Å
Rg (real space) rg_real	30.23 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	1.2630e+08
I(0) uncertainty (real space) i0_real_error	2.0570e+06
Rg (reciprocal space) rg_reciprocal	30.29 Å
I(0) (reciprocal space) i0_reciprocal	126300000.0000
Solution quality estimate total_estimate	0.9095
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.0 Å
Skewness Skewness skewness	0.133
Kurtosis Kurtosis kurtosis	-0.608
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31490000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. 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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8. Citations (1)

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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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus amyloliquefaciens
NCBI Class编号 ncbi_taxonomy_id	1390
宿主生物 host_organism	Escherichia coli

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

fit	/app/data/saxs_computation/rn/3rnz/3rnz.fit
pddf	/app/data/pr_computation/rn/3rnz/3rnz.pr.out
profile	/app/data/saxs_computation/rn/3rnz/3rnz.dat