SAXSdb — 4d7r

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

PROLINE/BETAINE TRANSPORTER, RALF

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	M9TGB4_RICPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 30–223； UniProt 2–195

PROLINE/BETAINE TRANSPORTER, RALF

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q8RT31

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8RT31_LEGPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 226–400； UniProt 200–374

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	4d7r
Deposition date deposition_date	2014-11-27
Structure title title	Crystal structure of a chimeric protein with the Sec7 domain of Rickettsia prowazekii RalF and the capping domain of Legionella pneumophila RalF
Keywords keywords	SIGNALING PROTEIN, GUANINE NUCLEOTIDE EXCHANGE FACTOR, BACTERIAL PATHOGENS, CHIMERIC PROTEIN; SIGNALING PROTEIN
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.

4d7r__assembly_1__model_1

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

Download this curve (.dat)

4d7r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4d7r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.44 Å
Rg (electron density)	22.46 Å
Total Rg	23.43 Å
Atom count	2870
Residues	355
Excluded volume	51332 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4d7r__assembly_1__model_1`	monomeric （1）	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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4d7ra1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.3 — Sec7 domain
Family Family family	a.118.3.0 — automated matches

Domain ID domain_id	d4d7ra2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.9 — RalF, C-terminal domain
Family Family family	d.129.9.1 — RalF, C-terminal domain

Domain ID domain_id	d4d7ra3
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

CATH v4.4 (3 domains)

Domain ID domain_id	4d7rA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4d7rA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1000 — Arf Nucleotide-binding Site Opener; domain 2
Homologous superfamily homologous superfamily	11 — Arf Nucleotide-binding Site Opener,domain 2

Domain ID domain_id	4d7rA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	140 — sec7 domains

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Unit-cell length a length_a	45.690 Å
Unit-cell length b length_b	94.840 Å
Unit-cell length c length_c	47.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	24.010 Å
R factor r_factor	0.1806
R_work r_work	0.1784
R_free r_free	0.2209

Description description	PROLINE/BETAINE TRANSPORTER, RALF
Molecular weight formula_weight	46002.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3338

Crystal structure of a chimeric protein with the Sec7 domain of Rickettsia prowazekii RalF and the capping domain of Legionella pneumophila RalF

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

PROLINE/BETAINE TRANSPORTER, RALF

State in the Current Structure

Other States of the Same Protein in the Database

PROLINE/BETAINE TRANSPORTER, RALF

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

4d7r__assembly_1__model_1

4d7r__assembly_1__model_1 | I(q)

4d7r__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	418

Crystal structure of a chimeric protein with the Sec7 domain of Rickettsia prowazekii RalF and the capping domain of Legionella pneumophila RalF

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

PROLINE/BETAINE TRANSPORTER, RALF

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROLINE/BETAINE TRANSPORTER, RALF

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

4d7r__assembly_1__model_1

4d7r__assembly_1__model_1 | I(q)

4d7r__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)