SAXSdb — 1a87

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

COLICIN N

Escherichia coli K12

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 67–387	Fragment：RECEPTOR-BINDING AND PORE-FORMING DOMAIN	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.10 Å R-free 0.310

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	CEAN_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–321； UniProt 67–387

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	1a87
Deposition date deposition_date	1998-04-03
Structure title title	COLICIN N
Keywords keywords	BACTERIOCIN, TOXIN, PORE-FORMING ACTIVITY; BACTERIOCIN
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	23.11 Å
Radius of gyration Rg (electron density) rg_electron	22.49 Å
Forward intensity I(0) i0	17389600.00
Molecular weight molecular_weight	32807.0 kDa
Excluded volume excluded_volume	41732 Å³
Envelope volume envelope_volume	49113 Å³
Hydration-shell volume shell_volume	19631 Å³
Envelope diameter envelope_diameter	79.5 Å
Shell Rg shell_rg	27.87 Å
Envelope Rg envelope_rg	22.53 Å
Shape Rg shape_rg	22.47 Å
Total Rg total_rg	23.29 Å
Total atoms total_atoms	2311
Residues n_residues	297
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	77.4 Å
Rg (real space) rg_real	23.26 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	1.7390e+07
I(0) uncertainty (real space) i0_real_error	2.6680e+05
Rg (reciprocal space) rg_reciprocal	23.23 Å
I(0) (reciprocal space) i0_reciprocal	17390000.0000
Solution quality estimate total_estimate	0.8529
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.521
Kurtosis Kurtosis kurtosis	-0.302
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4203000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.945

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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	d1a87a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.1 — Colicin
Family Family family	f.1.1.1 — Colicin

CATH v4.4 (2 domains)

Domain ID domain_id	1a87A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	60 — Colicin

Domain ID domain_id	1a87A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	30 — Colicin

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8. Citations (6)

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Unit-cell length a length_a	187.300 Å
Unit-cell length b length_b	187.300 Å
Unit-cell length c length_c	187.300 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	48

Space group space_group	I 41 3 2
Space-group number int_tables_number	214
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	23.000 Å
R factor r_factor	—
R_work r_work	0.1730
R_free r_free	0.3100

Description description	COLICIN N
Molecular weight formula_weight	35146.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2366

COLICIN N

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

COLICIN N

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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (6)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli K12
NCBI Class编号 ncbi_taxonomy_id	83333
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	55

fit	/app/data/saxs_computation/a8/1a87/1a87.fit
pddf	/app/data/pr_computation/a8/1a87/1a87.pr.out
profile	/app/data/saxs_computation/a8/1a87/1a87.dat