SAXSdb — 4udm

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

COLICIN-E3 IMMUNITY PROTEIN

ESCHERICHIA COLI BL21(DE3)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	COLICIN-E3 × 1 （P00646） CALCIUM ION × 3 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IMM3_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–85； UniProt 1–85

COLICIN-E3

ESCHERICHIA COLI BL21(DE3)

UniProt P00646

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	COLICIN-E3 IMMUNITY PROTEIN × 1 （P02984） CALCIUM ION × 3 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CEA3_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–96； UniProt 456–551

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	4udm
Deposition date deposition_date	2014-12-10
Structure title title	Crystal structure of Im3 in complex with Y52A mutant of E3RNase
Keywords keywords	;TRANSLATION, ANTIBIOTIC, ANTIMICROBIAL, BACTERIOCIN, BACTERIOCIN IMMUNITY, ENDONUCLEASE, HYDROLASE, INHIBITION, NUCLEASE, PROTEIN-PROTEIN INTERACTIONS, RIBONUCLEASE, RIBOSOME INACTIVATION, TOXIN ;; TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4udm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4udm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4udm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	17.15 Å
Rg (electron density)	16.06 Å
Total Rg	17.17 Å
Atom count	1455
Residues	180
Excluded volume	25554 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4udm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	COLICIN-E3 IMMUNITY PROTEIN
Molecular weight formula_weight	9910.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1490

MGLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW

Source Source

Source organism organism	ESCHERICHIA COLI BL21(DE3)
NCBI taxonomy ID ncbi_taxonomy_id	469008
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	COLICIN-E3
Molecular weight formula_weight	10720.0 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIAEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL

Source Source

Source organism organism	ESCHERICHIA COLI BL21(DE3)
NCBI taxonomy ID ncbi_taxonomy_id	469008
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4udma_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.2 — Colicin E3 immunity protein
Family Family family	d.26.2.1 — Colicin E3 immunity protein

Domain ID domain_id	d4udmb_
Class class	b — All beta proteins
Fold Fold fold	b.101 — Ribonuclease domain of colicin E3
Superfamily Superfamily superfamily	b.101.1 — Ribonuclease domain of colicin E3
Family Family family	b.101.1.1 — Ribonuclease domain of colicin E3

CATH v4.4 (2 domains)

Domain ID domain_id	4udmA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	20 — Cloacin immunity protein

Domain ID domain_id	4udmB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	380 — Ribonuclease domain of colicin e3 (Residues 456-551)
Homologous superfamily homologous superfamily	10 — Colicin E3-like ribonuclease domain

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Unit-cell length a length_a	92.854 Å
Unit-cell length b length_b	92.854 Å
Unit-cell length c length_c	76.942 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.960 Å
Low-resolution limit resolution_low	38.470 Å
R factor r_factor	0.1857
R_work r_work	0.1842
R_free r_free	0.2138

Crystal structure of Im3 in complex with Y52A mutant of E3RNase

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

COLICIN-E3 IMMUNITY PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

COLICIN-E3

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4udm__assembly_1__model_1

4udm__assembly_1__model_1 | I(q)

4udm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Im3 in complex with Y52A mutant of E3RNase

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

COLICIN-E3 IMMUNITY PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COLICIN-E3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4udm__assembly_1__model_1

4udm__assembly_1__model_1 | I(q)

4udm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)