SAXSdb — 6vj5

▼

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

PE-PGRS family protein PE25

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PPE family protein PPE41 × 1 （Q79FE1） ESX-5 secretion-associated protein EspG5 × 1 （B2HSU5） CHLORIDE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PE25_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–101； UniProt 1–99

PPE family protein PPE41

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt Q79FE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PE-PGRS family protein PE25 × 1 （I6X486） ESX-5 secretion-associated protein EspG5 × 1 （B2HSU5） CHLORIDE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPE41_MYCTU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–194； UniProt 1–194

ESX-5 secretion-associated protein EspG5

Mycobacterium marinum (strain ATCC BAA-535 / M)

UniProt B2HSU5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PE-PGRS family protein PE25 × 1 （I6X486） PPE family protein PPE41 × 1 （Q79FE1） CHLORIDE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ESPG5_MYCMM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–300； UniProt 1–300

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6vj5
Deposition date deposition_date	2020-01-14
Structure title title	Structure of PE25-PPE41(A124L) in complex with EspG5 chaperone from the type VII (ESX-5) secretion system
Keywords keywords	chaperone, protein secretion, mycobacteria, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6vj5__assembly_1__model_1

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

Download this curve (.dat)

6vj5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6vj5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.22 Å
Rg (electron density)	36.23 Å
Total Rg	36.32 Å
Atom count	8362
Residues	545
Excluded volume	74609 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6vj5__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PE-PGRS family protein PE25
Molecular weight formula_weight	10894.3 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	8571

GHMSFVITNPEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTGADKYATAEADNIKTFS

Source Source

Source organism organism	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	PPE family protein PPE41
Molecular weight formula_weight	22005.8 kDa
Mutation mutation	A124L
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHFEAYPPEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEAAKPFVRWLTDLCVQLSEVERQIHEIVRAYEWAHHDMVPLAQIYNNRAERQILIDNNLLGQFTAQIADLDQEYDDFWDEDGEVMRDYRLRVSDALSKLTPWKAPPPIAHSTVLVAPVSPSTASSRTDT

Source Source

Source organism organism	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	ESX-5 secretion-associated protein EspG5
Molecular weight formula_weight	32384.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MDQQSTRTDITVNVDGFWMLQALLDIRHVAPELRCRPYVSTDSNDWLNEHPGMAVMREQGIVVGDTVNEQVAARMRVLAAPDLEVVALLSRGKLLYGVVDNEDQPPGSRDIPDNEFRVVLARRGQHWVSAVRVGNDITVDDVSVSDSASIAALVIDGLESIHHADPAAINAVNVPLEEMLEATKSWQESGFNVFSGGDLRRMGISASTVAALGQALSDPAAEVAVYARQYRDDAKGPSASVLSLKDGSGGRIALYQQARTAGSGEAWLAICPATPQLVQVGVKTVLDTLPYGEWKTHSRV

Source Source

Source organism organism	Mycobacterium marinum (strain ATCC BAA-535 / M)
NCBI taxonomy ID ncbi_taxonomy_id	216594
Host organism host_organism	Escherichia coli BL21(DE3)

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	184

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6vj5a_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.4 — PE/PPE dimer-like
Family Family family	a.25.4.1 — PE

Domain ID domain_id	d6vj5b_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.4 — PE/PPE dimer-like
Family Family family	a.25.4.2 — PPE

▶

Unit-cell length a length_a	139.020 Å
Unit-cell length b length_b	139.020 Å
Unit-cell length c length_c	170.570 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	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	45.505 Å
R factor r_factor	0.2121
R_work r_work	0.2100
R_free r_free	0.2538

Structure of PE25-PPE41(A124L) in complex with EspG5 chaperone from the type VII (ESX-5) secretion system

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

PE-PGRS family protein PE25

State in the Current Structure

Other States of the Same Protein in the Database

PPE family protein PPE41

State in the Current Structure

Other States of the Same Protein in the Database

ESX-5 secretion-associated protein EspG5

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

6vj5__assembly_1__model_1

6vj5__assembly_1__model_1 | I(q)

6vj5__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Structure of PE25-PPE41(A124L) in complex with EspG5 chaperone from the type VII (ESX-5) secretion system

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

PE-PGRS family protein PE25

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PPE family protein PPE41

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ESX-5 secretion-associated protein EspG5

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

6vj5__assembly_1__model_1

6vj5__assembly_1__model_1 | I(q)

6vj5__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)