SAXSdb — 1a0j

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

TRYPSIN

OrganismNot specified

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 16–238 Chain B； UniProt 16–238 Chain C； UniProt 16–238 Chain D； UniProt 16–238	Not recorded	CA CALCIUM ION × 1 SO4 SULFATE ION × 10 BEN BENZAMIDINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；pH 4.6	Resolution 1.70 Å R-free 0.215
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 16–238 Chain B； UniProt 16–238 Chain C； UniProt 16–238 Chain D； UniProt 16–238	Not recorded	CA CALCIUM ION × 1 SO4 SULFATE ION × 10 BEN BENZAMIDINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；pH 4.6	Resolution 1.70 Å R-free 0.215

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	TRY3_SALSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–223； UniProt 16–238 Author chain B； PDBConstruct 1–223； UniProt 16–238 Author chain C； PDBConstruct 1–223； UniProt 16–238 Author chain D； PDBConstruct 1–223； UniProt 16–238

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	1a0j
Deposition date deposition_date	1997-12-01
Structure title title	CRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAPTED FISH SPECIES.
Keywords keywords	SERINE PROTEINASE, TRYPSIN, HYDROLASE, SERINE PROTEASE; SERINE PROTEASE
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	31.64 Å
Radius of gyration Rg (electron density) rg_electron	31.08 Å
Forward intensity I(0) i0	169152000.00
Molecular weight molecular_weight	96632.0 kDa
Excluded volume excluded_volume	117770 Å³
Envelope volume envelope_volume	145830 Å³
Hydration-shell volume shell_volume	39691 Å³
Envelope diameter envelope_diameter	109.2 Å
Shell Rg shell_rg	37.70 Å
Envelope Rg envelope_rg	30.89 Å
Shape Rg shape_rg	31.06 Å
Total Rg total_rg	31.61 Å
Total atoms total_atoms	6727
Residues n_residues	892
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	106.0 Å
Rg (real space) rg_real	31.73 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	1.6920e+08
I(0) uncertainty (real space) i0_real_error	2.9900e+06
Rg (reciprocal space) rg_reciprocal	31.69 Å
I(0) (reciprocal space) i0_reciprocal	169100000.0000
Solution quality estimate total_estimate	0.8750
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.0 Å
Skewness Skewness skewness	0.442
Kurtosis Kurtosis kurtosis	-0.220
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	64380000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.874

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	TRYPSIN
Molecular weight formula_weight	23803.7 kDa
EC 编号 ec_number	3.4.21.4
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7106

IVGGYECRKNSASYQASLQSGYHFCGGSLISSTWVVSAAHCYKSRIQVRLGEHNIAVNEGTEQFIDSVKVIMHPSYNSRNLDNDIMLIKLSKPASLNSYVSTVALPSSCASSGTRCLVSGWGNLSGSSSNYPDTLRCLDLPILSSSSCNSAYPGQITSNMFCAGFMEGGKDSCQGDSGGPVVCNGQLQGVVSWGYGCAQRNKPGVYTKVCNYRSWISSTMSSN

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	379

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a0ja_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d1a0jb_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d1a0jc_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d1a0jd_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (8 domains)

Domain ID domain_id	1a0jA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1a0jA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1a0jB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1a0jB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1a0jC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1a0jC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1a0jD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1a0jD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	65.907 Å
Unit-cell length b length_b	83.107 Å
Unit-cell length c length_c	154.787 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1730
R_work r_work	0.1730
R_free r_free	0.2150

fit	/app/data/saxs_computation/a0/1a0j/1a0j.fit
pddf	/app/data/pr_computation/a0/1a0j/1a0j.pr.out
profile	/app/data/saxs_computation/a0/1a0j/1a0j.dat

CRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAPTED FISH SPECIES.

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

TRYPSIN

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