SAXSdb — 1a2z

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

PYRROLIDONE CARBOXYL PEPTIDASE

Thermococcus litoralis

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 1–220 Chain B； UniProt 1–220 Chain C； UniProt 1–220 Chain D； UniProt 1–220	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 35% AMMONIUM SULFATE, 50 MM POTASSIUM PHOSPHATE, PH 6.5	Resolution 1.73 Å R-free 0.220

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PCP_THELI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–220； UniProt 1–220 Author chain B； PDBConstruct 1–220； UniProt 1–220 Author chain C； PDBConstruct 1–220； UniProt 1–220 Author chain D； PDBConstruct 1–220； UniProt 1–220

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	1a2z
Deposition date deposition_date	1998-01-13
Structure title title	PYRROLIDONE CARBOXYL PEPTIDASE FROM THERMOCOCCUS LITORALIS
Keywords keywords	PEPTIDASE, N-PYROGLUTAMATE HYDROLYSIS; PEPTIDASE
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	30.46 Å
Radius of gyration Rg (electron density) rg_electron	29.42 Å
Forward intensity I(0) i0	140064000.00
Molecular weight molecular_weight	99372.0 kDa
Excluded volume excluded_volume	126740 Å³
Envelope volume envelope_volume	148030 Å³
Hydration-shell volume shell_volume	41016 Å³
Envelope diameter envelope_diameter	97.5 Å
Shell Rg shell_rg	37.58 Å
Envelope Rg envelope_rg	29.32 Å
Shape Rg shape_rg	29.38 Å
Total Rg total_rg	30.30 Å
Total atoms total_atoms	6992
Residues n_residues	880
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	95.5 Å
Rg (real space) rg_real	30.34 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.4010e+08
I(0) uncertainty (real space) i0_real_error	2.0010e+06
Rg (reciprocal space) rg_reciprocal	30.40 Å
I(0) (reciprocal space) i0_reciprocal	140100000.0000
Solution quality estimate total_estimate	0.9047
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.9 Å
Skewness Skewness skewness	0.199
Kurtosis Kurtosis kurtosis	-0.537
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46670000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PYRROLIDONE CARBOXYL PEPTIDASE
Molecular weight formula_weight	24776.8 kDa
EC 编号 ec_number	3.4.19.3
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	7666

MKKVLITGFEPFGGDSKNPTEQIAKYFDRKQIGNAMVYGRVLPVSVKRATIELKRYLEEIKPEIVINLGLAPTYSNITVERIAVNIIDARIPDNDGYQPIDEKIEEDAPLAYMATLPVRAITKTLRDNGIPATISYSAGTYLCNYVMFKTLHFSKIEGYPLKAGFIHVPYTPDQVVNKFFLLGKNTPSMCLEAEIKAIELAVKVSLDYLEKDRDDIKIPL

来源 Source

来源生物 organism	Thermococcus litoralis
NCBI Class编号 ncbi_taxonomy_id	2265
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	660

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a2za_
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	d1a2zb_
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	d1a2zc_
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	d1a2zd_
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	1a2zA00
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	1a2zB00
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	1a2zC00
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	1a2zD00
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	91.644 Å
Unit-cell length b length_b	147.010 Å
Unit-cell length c length_c	71.553 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.730 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1800
R_free r_free	0.2200

fit	/app/data/saxs_computation/a2/1a2z/1a2z.fit
pddf	/app/data/pr_computation/a2/1a2z/1a2z.pr.out
profile	/app/data/saxs_computation/a2/1a2z/1a2z.dat

PYRROLIDONE CARBOXYL PEPTIDASE FROM THERMOCOCCUS LITORALIS

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

PYRROLIDONE CARBOXYL 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