2b5u

Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein

Method: X-RAY DIFFRACTION

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

Colicin E3

Escherichia coli

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） CITRIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Colicin E3 immunity protein × 1 （P02984） CITRIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CEA3_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–551； UniProt 1–551 Author chain C； PDBConstruct 1–551； UniProt 1–551

Colicin E3 immunity protein

Escherichia coli

UniProt P02984

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） CITRIC ACID × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Colicin E3 × 1 （P00646） CITRIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IMM3_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–84； UniProt 1–84 Author chain D； PDBConstruct 1–84； UniProt 1–84

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	2b5u
Deposition date deposition_date	2005-09-29
Structure title title	Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein
Keywords keywords	High resolution crystal structure, Colicin E3, Immunity Protein, Ribosome inactivation, RIBOSOME INHIBITOR, HYDROLASE; RIBOSOME INHIBITOR, HYDROLASE
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.

2b5u__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2b5u__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2b5u__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.57 Å
Rg (electron density)	36.25 Å
Total Rg	36.30 Å
Atom count	4286
Residues	554
Excluded volume	75112 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b5u__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2b5u__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Colicin E3
Molecular weight formula_weight	58047.0 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	V206C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8791

MSGGDGRGHNTGAHSTSGNINGGPTGLGVGGGASDGSGWSSENNPWGGGSGSGIHWGGGSGHGNGGGNGNSGGGSGTGGNLSAVAAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGPFKFGLWGVALYGVLPSQIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSCPVVDAKPTERPGVFTASIPGAPVLNISVNNSTPAVQTLSPGVTNNTDKDVRPAGFTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDKKRSAENNLNDEKNKPRKGFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli str. K12 substr. W3110

Entity 2 Entity 2 polymer

Description description	Colicin E3 immunity protein
Molecular weight formula_weight	9779.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli str. K12 substr. W3110

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2b5ua1
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

Domain ID domain_id	d2b5ua2
Class class	b — All beta proteins
Fold Fold fold	b.110 — Cloacin translocation domain
Superfamily Superfamily superfamily	b.110.1 — Cloacin translocation domain
Family Family family	b.110.1.1 — Cloacin translocation domain

Domain ID domain_id	d2b5ua3
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.9 — Colicin E3 receptor domain
Family Family family	h.4.9.1 — Colicin E3 receptor domain

Domain ID domain_id	d2b5ub_
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	d2b5uc1
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

Domain ID domain_id	d2b5uc2
Class class	b — All beta proteins
Fold Fold fold	b.110 — Cloacin translocation domain
Superfamily Superfamily superfamily	b.110.1 — Cloacin translocation domain
Family Family family	b.110.1.1 — Cloacin translocation domain

Domain ID domain_id	d2b5uc3
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.9 — Colicin E3 receptor domain
Family Family family	h.4.9.1 — Colicin E3 receptor domain

Domain ID domain_id	d2b5ud_
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

CATH v4.4 (6 domains)

Domain ID domain_id	2b5uA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	620 — Helix Hairpins

Domain ID domain_id	2b5uA03
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

Domain ID domain_id	2b5uB00
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	2b5uC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	620 — Helix Hairpins

Domain ID domain_id	2b5uC03
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

Domain ID domain_id	2b5uD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	20 — Cloacin immunity protein

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Unit-cell length a length_a	66.730 Å
Unit-cell length b length_b	192.916 Å
Unit-cell length c length_c	85.385 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	44.400 Å
R factor r_factor	0.2910
R_work r_work	0.2590
R_free r_free	0.2950

Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein

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

Colicin E3

State in the Current Structure

Other States of the Same Protein in the Database

Colicin E3 immunity protein

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

2b5u__assembly_2__model_1

2b5u__assembly_2__model_1 | I(q)

2b5u__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2b5u__assembly_2__model_1

2b5u__assembly_2__model_1 | I(q)

2b5u__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)