SAXSdb — 3cto

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

Uncharacterized protein Rv3357/MT3465

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 2 water × 4	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 water × 2	Consistent with protein count
11	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 1 water × 2	Consistent with protein count
12	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 water × 2	Consistent with protein count
13	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 2 water × 3	Consistent with protein count
14	Protein homooligomer	Homooligomer	Protein 2	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 2 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 2 water × 4	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 2 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 2 water × 4	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 2 water × 3	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	water × 1	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 1 water × 2	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
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 1–91 Author chain B； PDBConstruct 1–91； UniProt 1–91 Author chain C； PDBConstruct 1–91； UniProt 1–91 Author chain D； PDBConstruct 1–91； UniProt 1–91 Author chain E； PDBConstruct 1–91； UniProt 1–91

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	3cto
Deposition date deposition_date	2008-04-14
Structure title title	Crystal Structure of M. tuberculosis YefM antitoxin
Keywords keywords	Homotetramer, toxin inhibitor; TOXIN INHIBITOR
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.

3cto__assembly_7__model_1

Assembly 7 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3cto__assembly_7__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cto__assembly_7__model_1 | P(r) · Pending

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

Rg（Guinier）	23.41 Å
Rg (electron density)	22.73 Å
Total Rg	23.51 Å
Atom count	1727
Residues	216
Excluded volume	30162 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cto__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cto__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3cto__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3cto__assembly_4__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3cto__assembly_5__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3cto__assembly_6__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3cto__assembly_7__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3cto__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3cto__assembly_9__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3cto__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3cto__assembly_11__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3cto__assembly_12__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`3cto__assembly_13__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`3cto__assembly_14__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 (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein Rv3357/MT3465
Molecular weight formula_weight	10207.3 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	2584

MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREMAGGEE

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	59

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3ctoa_
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	d3ctob_
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	d3ctoc_
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	d3ctod_
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	d3ctoe_
Class class	j — Peptides
Fold Fold fold	j.124 — YefM fragments
Superfamily Superfamily superfamily	j.124.1 — YefM fragments
Family Family family	j.124.1.1 — YefM fragments

CATH v4.4 (7 domains)

Domain ID domain_id	3ctoA01
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	3ctoA02
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	3ctoB01
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	3ctoB02
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	3ctoC01
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	3ctoC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3ctoD00
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

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Unit-cell length a length_a	65.003 Å
Unit-cell length b length_b	64.573 Å
Unit-cell length c length_c	83.518 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	20

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.2077
R_work r_work	0.2053
R_free r_free	0.2545

Crystal Structure of M. tuberculosis YefM antitoxin

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

Uncharacterized protein Rv3357/MT3465

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

3cto__assembly_7__model_1

3cto__assembly_7__model_1 | I(q)

3cto__assembly_7__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Crystal Structure of M. tuberculosis YefM antitoxin

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

Uncharacterized protein Rv3357/MT3465

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

3cto__assembly_7__model_1

3cto__assembly_7__model_1 | I(q)

3cto__assembly_7__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

CATH v4.4 (7 domains)

7. Citations (1)