SAXSdb — 4yg7

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

Antitoxin HipB

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	Serine/threonine-protein kinase HipA × 2 （P23874） DNA (50-MER) × 1 DNA (50-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIPB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–71； UniProt 4–74 Author chain C； PDBConstruct 1–71； UniProt 4–74 Author chain E； PDBConstruct 1–71； UniProt 4–74 Author chain G； PDBConstruct 1–71； UniProt 4–74

Serine/threonine-protein kinase HipA

Escherichia coli (strain K12)

UniProt P23874

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	Antitoxin HipB × 4 （P23873） DNA (50-MER) × 1 DNA (50-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIPA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–436； UniProt 2–437 Author chain K； PDBConstruct 1–436； UniProt 2–437

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	4yg7
Deposition date deposition_date	2015-02-25
Structure title title	Structure of FL autorepression promoter complex
Keywords keywords	persistence, multidrug tolerance, autorepression, promoter, TRANSCRIPTION, TRANSFERASE-DNA complex; TRANSCRIPTION, TRANSFERASE/DNA
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.

4yg7__assembly_1__model_1

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

Download this curve (.dat)

4yg7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yg7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.23 Å
Rg (electron density)	37.83 Å
Total Rg	38.38 Å
Atom count	10806
Residues	1206
Excluded volume	187230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yg7__assembly_1__model_1`	octameric （8）	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 (4)

Entity 1 Entity 1 polymer

Description description	Antitoxin HipB
Molecular weight formula_weight	8060.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,C,G
Atom count atom_count	10806

FQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAK

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Serine/threonine-protein kinase HipA
Molecular weight formula_weight	48946.2 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,K

PKLVTWMNNQRVGELTKLANGAHTFKYAPEWLASRYARPLSLSLPLQRGNITSDAVFNFFDNLLPDSPIVRDRIVKRYHAKSRQPFDLLSEIGRDSVGAVTLIPEDETVTHPIMAWEKLTEARLEEVLTAYKADIPLGMIREENDFRISVAGAQEKTALLRIGNDWCIPKGITPTTHIIKLPIGEIRQPNATLDLSQSVDNEYYCLLLAKELGLNVPDAEIIKAGNVRALAVERFDRRWNAERTVLLRLPQEDMCQTFGLPSSVKYESDGGPGIARIMAFLMGSSEALKDRYDFMKFQVFQWLIGATQGHAKNFSVFIQAGGSYRLTPFYDIISAFPVLGGTGIHISDLKLAMGLNASKGKKTAIDKIYPRHFLATAKVLRFPEVQMHEILSDFARMIPAALDNVKTSLPTDFPENVVTAVESNVLRLHGRLSREY

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA (50-MER)
Molecular weight formula_weight	15398.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	R

GCTTATCCCCTTAAGGGGATATATATATATATATCCCCTTAAGGGGATAA

Entity 4 Entity 4 polymer

Description description	DNA (50-MER)
Molecular weight formula_weight	15414.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

GCTTATCCCCTTAAGGGGATATATATATATATATCCCCTTAAGGGGATAG

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4yg7B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	4yg7C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	4yg7E00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	4yg7G00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

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Unit-cell length a length_a	228.200 Å
Unit-cell length b length_b	228.200 Å
Unit-cell length c length_c	130.800 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.770 Å
Low-resolution limit resolution_low	161.400 Å
R factor r_factor	—
R_work r_work	0.3837
R_free r_free	0.3785

Structure of FL autorepression promoter complex

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

Antitoxin HipB

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein kinase HipA

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

4yg7__assembly_1__model_1

4yg7__assembly_1__model_1 | I(q)

4yg7__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 (4)

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

Entity 4 Entity 4 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of FL autorepression promoter complex

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

Antitoxin HipB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein kinase HipA

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

4yg7__assembly_1__model_1

4yg7__assembly_1__model_1 | I(q)

4yg7__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 (4)

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

Entity 4 Entity 4 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)