SAXSdb — 7d98

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

LysR-type regulatory protein

Cupriavidus necator

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 4 DNA 2	DNA (56-mer) × 1 DNA (56-mer) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXC7_CUPNE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–294； UniProt 1–294 Author chain B； PDBConstruct 1–294； UniProt 1–294 Author chain P； PDBConstruct 1–294； UniProt 1–294 Author chain Q； PDBConstruct 1–294； UniProt 1–294

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	7d98
Deposition date deposition_date	2020-10-12
Structure title title	Crystal structure of full-length CbnR complexed with the target DNA complex
Keywords keywords	LysR-type regulatory protein, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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.

7d98__assembly_1__model_1

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

Download this curve (.dat)

7d98__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7d98__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.81 Å
Rg (electron density)	38.19 Å
Total Rg	38.83 Å
Atom count	9258
Residues	1201
Excluded volume	161370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7d98__assembly_1__model_1`	hexameric （6）	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	LysR-type regulatory protein
Molecular weight formula_weight	32085.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,P,Q
Atom count atom_count	9258

MEFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAGAASSIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKEKQPPILARFVEHVRRSAKD

Source Source

Source organism organism	Cupriavidus necator
Common name common_name	Alcaligenes eutrophus
NCBI taxonomy ID ncbi_taxonomy_id	106590
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA (56-mer)
Molecular weight formula_weight	17319.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

ACTATATTACGCAAACCGTAACGATGGCTGACTAATTTGGTATTGGACGGCATGGC

Entity 3 Entity 3 polymer

Description description	DNA (56-mer)
Molecular weight formula_weight	17190.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

TGCCATGCCGTCCAATACCAAATTAGTCAGCCATCGTTACGGTTTGCGTAATATAG

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Unit-cell length a length_a	105.819 Å
Unit-cell length b length_b	105.819 Å
Unit-cell length c length_c	602.516 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	48

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

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2370
R_work r_work	0.2344
R_free r_free	0.2861

Crystal structure of full-length CbnR complexed with the target DNA complex

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

LysR-type 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

7d98__assembly_1__model_1

7d98__assembly_1__model_1 | I(q)

7d98__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Citations (1)

Crystal structure of full-length CbnR complexed with the target DNA complex

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

LysR-type 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

7d98__assembly_1__model_1

7d98__assembly_1__model_1 | I(q)

7d98__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

7. Citations (1)