SAXSdb — 2bnz

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

ORF OMEGA

STREPTOCOCCUS PYOGENES

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 4 DNA 4	;5'-D(GPAPAPTPCPAPCPAPAPGP TPGPAPTPTPAPGPC)-3' ; × 2 ;5'-D(CPTPAPAPTPCPAPCPTPTP GPTPGPAPTPTPCPG)-3' ; × 2 water × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q57468_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–53； UniProt 20–71 Author chain B； PDBConstruct 2–53； UniProt 20–71 Author chain C； PDBConstruct 2–53； UniProt 20–71 Author chain D； PDBConstruct 2–53； UniProt 20–71

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	2bnz
Deposition date deposition_date	2005-04-06
Structure title title	Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats
Keywords keywords	DNA BINDING PROTEIN-DNA COMPLEX, RIBBON-HELIX-HELIX, RHH, METJ/ARC SUPERFAMILY, COOPERATIVE DNA BINDING, INC18 FAMILY; 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.

2bnz__assembly_1__model_1

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

Download this curve (.dat)

2bnz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bnz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.86 Å
Rg (electron density)	23.49 Å
Total Rg	24.07 Å
Atom count	2540
Residues	244
Excluded volume	42541 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bnz__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	ORF OMEGA
Molecular weight formula_weight	6137.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2585

MAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL

Source Source

Source organism organism	STREPTOCOCCUS PYOGENES
NCBI taxonomy ID ncbi_taxonomy_id	1314
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	;5'-D(GPAPAPTPCPAPCPAPAPGP TPGPAPTPTPAPGPC)-3' ;
Molecular weight formula_weight	5548.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G

GAATCACAAGTGATTAGC

Entity 3 Entity 3 polymer

Description description	;5'-D(CPTPAPAPTPCPAPCPTPTP GPTPGPAPTPTPCPG)-3' ;
Molecular weight formula_weight	5481.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H

CTAATCACTTGTGATTCG

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2bnza_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.4 — Omega transcriptional repressor

Domain ID domain_id	d2bnzb_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.4 — Omega transcriptional repressor

Domain ID domain_id	d2bnzc_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.4 — Omega transcriptional repressor

Domain ID domain_id	d2bnzd_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.4 — Omega transcriptional repressor

CATH v4.4 (4 domains)

Domain ID domain_id	2bnzA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	2bnzB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	2bnzC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	2bnzD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

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Unit-cell length a length_a	75.991 Å
Unit-cell length b length_b	42.505 Å
Unit-cell length c length_c	103.727 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.17 °
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	2.600 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.2270
R_work r_work	0.2250
R_free r_free	0.2580

Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats

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

ORF OMEGA

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

2bnz__assembly_1__model_1

2bnz__assembly_1__model_1 | I(q)

2bnz__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats

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

ORF OMEGA

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

2bnz__assembly_1__model_1

2bnz__assembly_1__model_1 | I(q)

2bnz__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)