SAXSdb — 4gpg

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

Protease 1

Achromobacter lyticus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 206–473	Not recorded	No other associated polymer	Experimental method not declared X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；297 K；20% w/v PEG 3350, 10mM Tris, HCl pH 8.0, 50% PEG 3350, HCl pD 8.0, VAPOR DIFFUSION, temperature 297K	Resolution not provided

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 4GPG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ARB THE PRIMARY STRUCTURE AND STRUCTURAL CHARACTERISTICS OF ACHROMOBACTER LYTICUS PROTEASE I, A LYSINE-SPECIFIC SERINE PROTEASE Deposited 1993-04-15	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 206–473（268 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.20 Å
1ARC THE PRIMARY STRUCTURE AND STRUCTURAL CHARACTERISTICS OF ACHROMOBACTER LYTICUS PROTEASE I, A LYSINE-SPECIFIC SERINE PROTEASE Deposited 1993-04-15	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 206–473（268 aa） Fragment：residues 206-473	Not recorded	TCK N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å

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

View Construct and Data Evidence

UniProt name	API_ACHLY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–268； UniProt 206–473

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	4gpg
Deposition date deposition_date	2012-08-21
Structure title title	X/N joint refinement of Achromobacter Lyticus Protease I free form at pD8.0
Keywords keywords	lysine specific serine protease, HYDROLASE; HYDROLASE

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

Radius of gyration Rg (Guinier) rg_guinier	18.02 Å
Radius of gyration Rg (electron density) rg_electron	16.79 Å
Forward intensity I(0) i0	18270100.00
Molecular weight molecular_weight	30244.0 kDa
Excluded volume excluded_volume	36491 Å³
Envelope volume envelope_volume	40260 Å³
Hydration-shell volume shell_volume	19157 Å³
Envelope diameter envelope_diameter	56.1 Å
Shell Rg shell_rg	23.88 Å
Envelope Rg envelope_rg	17.26 Å
Shape Rg shape_rg	16.95 Å
Total Rg total_rg	17.26 Å
Total atoms total_atoms	4014
Residues n_residues	263
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	52.2 Å
Rg (real space) rg_real	17.84 Å
Rg uncertainty (real space) rg_real_error	0.06 Å
I(0) (real space) i0_real	1.7620e+07
I(0) uncertainty (real space) i0_real_error	1.5540e+05
Rg (reciprocal space) rg_reciprocal	17.88 Å
I(0) (reciprocal space) i0_reciprocal	18270000.0000
Solution quality estimate total_estimate	0.7170
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.075
Kurtosis Kurtosis kurtosis	-0.495
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	11.1200
Highest regularization parameter α highest_alpha	3706000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 0.914; Sysdev: 0.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.725

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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4gpga_
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.47.1.1 — Prokaryotic proteases

CATH v4.4 (2 domains)

Domain ID domain_id	4gpgA01
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	4gpgA02
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	39.574 Å
Unit-cell length b length_b	40.785 Å
Unit-cell length c length_c	43.980 Å
Unit-cell angle α angle_alpha	64.82 °
Unit-cell angle β angle_beta	66.10 °
Unit-cell angle γ angle_gamma	73.42 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	Protease 1
Molecular weight formula_weight	27759.2 kDa
EC 编号 ec_number	3.4.21.50
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4270

来源生物 organism	Achromobacter lyticus
NCBI Class编号 ncbi_taxonomy_id	224
宿主生物 host_organism	Escherichia coli

X/N joint refinement of Achromobacter Lyticus Protease I free form at pD8.0

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

Protease 1

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

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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	140

fit	/app/data/saxs_computation/gp/4gpg/4gpg.fit
pddf	/app/data/pr_computation/gp/4gpg/4gpg.pr.out
profile	/app/data/saxs_computation/gp/4gpg/4gpg.dat