3oei

Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3)

Method: X-RAY DIFFRACTION

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

RelJ (Antitoxin Rv3357)

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RelK (Toxin Rv3358) × 2 （P64528） CITRATE ANION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	RelK (Toxin Rv3358) × 2 （P64528） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	RelK (Toxin Rv3358) × 2 （P64528） water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	RelK (Toxin Rv3358) × 2 （P64528） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y3357_MYCTU
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 1–91 Author chain B； PDBConstruct 1–91； UniProt 1–91 Author chain I； PDBConstruct 1–91； UniProt 1–91 Author chain J； PDBConstruct 1–91； UniProt 1–91 Author chain M； PDBConstruct 1–91； UniProt 1–91 Author chain N； PDBConstruct 1–91； UniProt 1–91 Author chain E； PDBConstruct 1–91； UniProt 1–91 Author chain F； PDBConstruct 1–91； UniProt 1–91

RelK (Toxin Rv3358)

Mycobacterium tuberculosis

UniProt P64528

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	RelJ (Antitoxin Rv3357) × 2 （P65067） CITRATE ANION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	RelJ (Antitoxin Rv3357) × 2 （P65067） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	RelJ (Antitoxin Rv3357) × 2 （P65067） water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	RelJ (Antitoxin Rv3357) × 2 （P65067） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y3358_MYCTU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 13–96； UniProt 2–85 Author chain D； PDBConstruct 13–96； UniProt 2–85 Author chain G； PDBConstruct 13–96； UniProt 2–85 Author chain H； PDBConstruct 13–96； UniProt 2–85 Author chain K； PDBConstruct 13–96； UniProt 2–85 Author chain L； PDBConstruct 13–96； UniProt 2–85 Author chain O； PDBConstruct 13–96； UniProt 2–85 Author chain P； PDBConstruct 13–96； UniProt 2–85

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	3oei
Deposition date deposition_date	2010-08-12
Structure title title	Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3)
Keywords keywords	;Toxin-antitoxin systems, Protein-protein complex, Tuberculosis Structural Genomics Consortium, Toxin, Protein Binding, TB Structural Genomics Consortium, TBSGC ;; Toxin, Protein Binding
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.

3oei__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3oei__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3oei__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	23.88 Å
Rg (electron density)	22.98 Å
Total Rg	23.83 Å
Atom count	2732
Residues	335
Excluded volume	47841 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3oei__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3oei__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3oei__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3oei__assembly_4__model_1`	tetrameric （4）	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	RelJ (Antitoxin Rv3357)
Molecular weight formula_weight	10876.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,I,J,M,N
Atom count atom_count	11529

MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREMAGGEEMQAGPAL

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RelK (Toxin Rv3358)
Molecular weight formula_weight	11504.7 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,H,K,L,O,P

HHHHHHDDDDKVRSVNFDPDAWEDFLFWLAADRKTARRITRLIGEIQRDPFSGIGKPEPLQGELSGYWSRRIDDEHRLVYRAGDDEVTMLKARYHY

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	RelJ (Antitoxin Rv3357)
Molecular weight formula_weight	10889.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREMAGGEEMQAGPAL

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 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	420

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6. Fold Classification (SCOP + CATH) 43 domains

SCOP 2.08 (19 domains)

Domain ID domain_id	d3oeia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.0 — automated matches

Domain ID domain_id	d3oeib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.0 — automated matches

Domain ID domain_id	d3oeic1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.0 — automated matches

Domain ID domain_id	d3oeic2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3oeid1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.0 — automated matches

Domain ID domain_id	d3oeid2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3oeie_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.0 — automated matches

Domain ID domain_id	d3oeif_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.0 — automated matches

Domain ID domain_id	d3oeig_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.0 — automated matches

Domain ID domain_id	d3oeih1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.0 — automated matches

Domain ID domain_id	d3oeih2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3oeii_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.0 — automated matches

Domain ID domain_id	d3oeij_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.0 — automated matches

Domain ID domain_id	d3oeik_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.0 — automated matches

Domain ID domain_id	d3oeil_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.0 — automated matches

Domain ID domain_id	d3oeim_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.0 — automated matches

Domain ID domain_id	d3oein_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.306 — YefM-like
Superfamily Superfamily superfamily	d.306.1 — YefM-like
Family Family family	d.306.1.0 — automated matches

Domain ID domain_id	d3oeio_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.0 — automated matches

Domain ID domain_id	d3oeip_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.298 — RelE-like
Superfamily Superfamily superfamily	d.298.1 — RelE-like
Family Family family	d.298.1.0 — automated matches

CATH v4.4 (24 domains)

Domain ID domain_id	3oeiA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	3oeiA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	3oeiB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	3oeiB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	3oeiC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

Domain ID domain_id	3oeiD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

Domain ID domain_id	3oeiE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	3oeiE02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	3oeiF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	3oeiF02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	3oeiG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

Domain ID domain_id	3oeiH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

Domain ID domain_id	3oeiI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	3oeiI02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	3oeiJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	3oeiJ02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	3oeiK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

Domain ID domain_id	3oeiL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

Domain ID domain_id	3oeiM01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	3oeiM02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	3oeiN01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	3oeiN02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	330 —

Domain ID domain_id	3oeiO00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

Domain ID domain_id	3oeiP00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	20 — RelE-like

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Unit-cell length a length_a	42.219 Å
Unit-cell length b length_b	187.512 Å
Unit-cell length c length_c	113.881 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.145 Å
Low-resolution limit resolution_low	40.506 Å
R factor r_factor	0.2058
R_work r_work	0.2031
R_free r_free	0.2559

Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3)

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

RelJ (Antitoxin Rv3357)

State in the Current Structure

Other States of the Same Protein in the Database

RelK (Toxin Rv3358)

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

3oei__assembly_4__model_1

3oei__assembly_4__model_1 | I(q)

3oei__assembly_4__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 43 domains

SCOP 2.08 (19 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3)

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

RelJ (Antitoxin Rv3357)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RelK (Toxin Rv3358)

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

3oei__assembly_4__model_1

3oei__assembly_4__model_1 | I(q)

3oei__assembly_4__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 43 domains

SCOP 2.08 (19 domains)

CATH v4.4 (24 domains)

7. Citations (1)