SAXSdb — 4d7q

▼

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

RALF, PROLINE/BETAINE TRANSPORTER

RICKETTSIA PROWAZEKII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 NITRATE ION × 1 GLYCEROL × 4 DI(HYDROXYETHYL)ETHER × 2 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 197–344； UniProt 189–336

RALF, PROLINE/BETAINE TRANSPORTER

RICKETTSIA PROWAZEKII

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	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 NITRATE ION × 1 GLYCEROL × 4 DI(HYDROXYETHYL)ETHER × 2 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 8–196； UniProt 2–190

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	4d7q
Deposition date deposition_date	2014-11-27
Structure title title	Crystal structure of a chimeric protein with the Sec7 domain of Legionella pneumophila RalF and the capping domain of Rickettsia prowazekii RalF
Keywords keywords	SIGNALING PROTEIN, GUANINE NUCLEOTIDE EXCHANGE FACTOR, BACTERIAL PATHOGENS; SIGNALING PROTEIN
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.

4d7q__assembly_1__model_1

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

Download this curve (.dat)

4d7q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4d7q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.91 Å
Rg (electron density)	21.72 Å
Total Rg	22.63 Å
Atom count	2938
Residues	347
Excluded volume	51090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4d7q__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	RALF, PROLINE/BETAINE TRANSPORTER
Molecular weight formula_weight	40515.7 kDa
Mutation mutation	YES
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	3214

MKHHHHHHPEIEKAQREIIEAFNAKPKNGINKIKEICEQYKISPNEEIAEFFHQQRKNLDLEAVGDYLSSPEAENQQVLKAFTSQMNFNGQSFVEGLRTFLKTFKLPGEAQKIDRLVQSFSGAYFQQNPDVVSNADAAYLLAFQTIMLNTDLHNPSIPEKNKMTVYGLKRNLRGGNNGGDFDAKFLEELYSEIKAKPFELNFVDSSPGYQINNISSQNDKTFKQLNQFLEEKRNIQNIFPKLQNNNLTIEFKNPKTFLSKFTGYKGSVIIKDEKSGAAEIQVYKPSIFSRWFLGEKSKIIIQPLREEGRQPSEQSLKLAAQITASFETKVTSIKATYDYLKEDLKSQYDNIR

Source Source

Source organism organism	RICKETTSIA PROWAZEKII
NCBI taxonomy ID ncbi_taxonomy_id	272947
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	268

▼

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4d7qA01
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	4d7qA02
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	4d7qA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	140 — sec7 domains

▶

Unit-cell length a length_a	40.310 Å
Unit-cell length b length_b	77.440 Å
Unit-cell length c length_c	119.110 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	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	38.720 Å
R factor r_factor	0.1773
R_work r_work	0.1752
R_free r_free	0.2168

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

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

RALF, PROLINE/BETAINE TRANSPORTER

State in the Current Structure

Other States of the Same Protein in the Database

RALF, PROLINE/BETAINE TRANSPORTER

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

4d7q__assembly_1__model_1

4d7q__assembly_1__model_1 | I(q)

4d7q__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

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

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

RALF, PROLINE/BETAINE TRANSPORTER

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RALF, PROLINE/BETAINE TRANSPORTER

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

4d7q__assembly_1__model_1

4d7q__assembly_1__model_1 | I(q)

4d7q__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)