7oyk

DNA-binding domain of CggR in complex with the DNA operator

Method: X-RAY DIFFRACTION

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

Central glycolytic genes regulator

Bacillus subtilis (strain 168)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	DNA operator - strand 1 × 1 DNA operator - strand 2 × 1 CALCIUM ION × 1 PHOSPHATE ION × 1 water × 4	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 4	DNA operator - strand 1 × 2 DNA operator - strand 2 × 2 CALCIUM ION × 1 1,2-ETHANEDIOL × 1 PHOSPHATE ION × 1 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CGGR_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 6–96； UniProt 1–91 Author chain BBB； PDBConstruct 6–96； UniProt 1–91 Author chain CCC； PDBConstruct 6–96； UniProt 1–91 Author chain DDD； PDBConstruct 6–96； UniProt 1–91

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	7oyk
Deposition date deposition_date	2021-06-24
Structure title title	DNA-binding domain of CggR in complex with the DNA operator
Keywords keywords	Transcriptional repressor, Glycolysis, Helix-turn-helix domain, Bacillus subtilis, DNA BINDING PROTEIN; 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.

7oyk__assembly_1__model_1

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

Download this curve (.dat)

7oyk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7oyk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.65 Å
Rg (electron density)	21.52 Å
Total Rg	22.21 Å
Atom count	2182
Residues	216
Excluded volume	37322 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7oyk__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7oyk__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Central glycolytic genes regulator
Molecular weight formula_weight	11121.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,DDD,CCC,BBB
Atom count atom_count	5175

SNAASMNQLIQAQKKLLPDLLLVMQKRFEILQYIRLTEPIGRRSLSASLGISERVLRGEVQFLKEQNLVDIKTNGMTLTEEGYELLSVLEDTMKDV

Source Source

Source organism organism	Bacillus subtilis (strain 168)
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA operator - strand 1
Molecular weight formula_weight	4885.2 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	EEE,LLL,GGG

GACAAAAAACGTCCCG

Entity 3 Entity 3 polymer

Description description	DNA operator - strand 2
Molecular weight formula_weight	4911.2 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	FFF,KKK,HHH

CGGGACGTTTTTTGTC

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	139

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Unit-cell length a length_a	57.972 Å
Unit-cell length b length_b	103.141 Å
Unit-cell length c length_c	51.111 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.101 Å
Low-resolution limit resolution_low	45.837 Å
R factor r_factor	—
R_work r_work	0.2080
R_free r_free	0.2527

DNA-binding domain of CggR in complex with the DNA operator

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

Central glycolytic genes regulator

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

7oyk__assembly_1__model_1

7oyk__assembly_1__model_1 | I(q)

7oyk__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

DNA-binding domain of CggR in complex with the DNA operator

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

Central glycolytic genes regulator

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

7oyk__assembly_1__model_1

7oyk__assembly_1__model_1 | I(q)

7oyk__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)