SAXSdb — 5f1r

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

Listeriolysin regulatory protein

Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(3~{R})-8-cyclopropyl-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRFA_LISMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–237； UniProt 1–237 Author chain B； PDBConstruct 1–237； UniProt 1–237

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	5f1r
Deposition date deposition_date	2015-11-30
Structure title title	The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (C10)
Keywords keywords	DNA Binding Protein, PrfA, 2-pyridones, Virulence; DNA BINDING 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.

5f1r__assembly_1__model_1

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

Download this curve (.dat)

5f1r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5f1r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.90 Å
Rg (electron density)	22.55 Å
Total Rg	23.62 Å
Atom count	7578
Residues	458
Excluded volume	68665 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5f1r__assembly_1__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	Listeriolysin regulatory protein
Molecular weight formula_weight	27329.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7602

MNAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN

Source Source

Source organism organism	Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
NCBI taxonomy ID ncbi_taxonomy_id	169963
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(3~{R})-8-cyclopropyl-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid
Molecular weight formula_weight	377.5 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	22

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5f1rA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	5f1rA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	5f1rB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	5f1rB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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Unit-cell length a length_a	56.340 Å
Unit-cell length b length_b	80.970 Å
Unit-cell length c length_c	62.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	57.578 Å
R factor r_factor	0.2029
R_work r_work	0.1978
R_free r_free	0.2594

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (C10)

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

Listeriolysin regulatory protein

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

5f1r__assembly_1__model_1

5f1r__assembly_1__model_1 | I(q)

5f1r__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (C10)

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

Listeriolysin regulatory protein

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

5f1r__assembly_1__model_1

5f1r__assembly_1__model_1 | I(q)

5f1r__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)