SAXSdb — 1col

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

COLICIN A

Escherichia coli

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 389–592	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 389–592	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å

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	CEA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–204； UniProt 389–592 Author chain B； PDBConstruct 1–204； UniProt 389–592

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	1col
Deposition date deposition_date	1991-07-06
Structure title title	REFINED STRUCTURE OF THE PORE-FORMING DOMAIN OF COLICIN A AT 2.4 ANGSTROMS RESOLUTION
Keywords keywords	ANTIBACTERIAL PROTEIN; ANTIBACTERIAL PROTEIN
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	25.25 Å
Radius of gyration Rg (electron density) rg_electron	24.59 Å
Forward intensity I(0) i0	28617800.00
Molecular weight molecular_weight	42075.0 kDa
Excluded volume excluded_volume	53230 Å³
Envelope volume envelope_volume	62352 Å³
Hydration-shell volume shell_volume	22569 Å³
Envelope diameter envelope_diameter	86.1 Å
Shell Rg shell_rg	30.17 Å
Envelope Rg envelope_rg	24.68 Å
Shape Rg shape_rg	24.57 Å
Total Rg total_rg	25.36 Å
Total atoms total_atoms	2956
Residues n_residues	394
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	83.4 Å
Rg (real space) rg_real	25.40 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	2.8620e+07
I(0) uncertainty (real space) i0_real_error	4.7150e+05
Rg (reciprocal space) rg_reciprocal	25.36 Å
I(0) (reciprocal space) i0_reciprocal	28620000.0000
Solution quality estimate total_estimate	0.8409
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.515
Kurtosis Kurtosis kurtosis	-0.381
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9562000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.716; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.848; Smooth: 0.932

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cola_
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

Domain ID domain_id	d1colb_
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	1colA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	30 — Colicin

Domain ID domain_id	1colB00
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 (7)

Refined structure of the pore-forming domain of colicin A at 2.4 A resolution.

J.Mol.Biol. (1992)

PMID: 1373773 · DOI: 10.1016/0022-2836(92)90550-4 PRIMARY

Fluorescence Energy Transfer Distance Measurements Using Site-Directed Single Cysteine Mutants

J.Mol.Biol. (1991)

Colicins: Prokaryotic Killer-Pores

Experientia (1990)

Structure of the Membrane-Pore-Forming Fragment of Colicin A

Nature (1989)

The Membrane Channel-Forming Colicin A: Synthesis, Secretion, Structure, Action and Immunity

Biochim.Biophys.Acta (1988)

Gating Processes of Channels Induced by Colicin A, its C-Terminal Fragment and Colicin E1 in Planar Lipid Bilayers

Eur.Biophys.J. (1987)

Crystallization of the C-Terminal Domain of Colicin A Carrying the Voltage-Dependent Pore Activity of the Protein

J.Mol.Biol. (1986)

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Unit-cell length a length_a	73.000 Å
Unit-cell length b length_b	73.000 Å
Unit-cell length c length_c	171.600 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1800
R_work r_work	—
R_free r_free	—

Description description	COLICIN A
Molecular weight formula_weight	21818.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3039

REFINED STRUCTURE OF THE PORE-FORMING DOMAIN OF COLICIN A AT 2.4 ANGSTROMS RESOLUTION

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

COLICIN A

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

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (7)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	83

fit	/app/data/saxs_computation/co/1col/1col.fit
pddf	/app/data/pr_computation/co/1col/1col.pr.out
profile	/app/data/saxs_computation/co/1col/1col.dat