1bdx

E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY

Method: X-RAY DIFFRACTION

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

HOLLIDAY JUNCTION DNA HELICASE RUVA

Escherichia coli BL21(DE3)

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	;DNA (5'-D(PGPCPAPTPGPCPAPTPAPTPGPCPAPTPGPC)-3') ; × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUVA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 1–203 Author chain B； PDBConstruct 1–203； UniProt 1–203 Author chain C； PDBConstruct 1–203； UniProt 1–203 Author chain D； PDBConstruct 1–203； UniProt 1–203

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	1bdx
Deposition date deposition_date	1998-05-11
Structure title title	E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY
Keywords keywords	DNA-BINDING, BRANCH MIGRATION, HOLLIDAY JUNCTION, RUV, COMPLEX DNA-BINDING PROTEIN-DNA, TRANSFERASE-DNA COMPLEX; 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.

1bdx__assembly_1__model_1

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

Download this curve (.dat)

1bdx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1bdx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.56 Å
Rg (electron density)	29.40 Å
Total Rg	29.81 Å
Atom count	64
Residues	64
Excluded volume	104190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1bdx__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 (2)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(PGPCPAPTPGPCPAPTPAPTPGPCPAPTPGPC)-3') ;
Molecular weight formula_weight	4898.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,K,L,M
Atom count atom_count	824

GCATGCATATGCATGC

Entity 2 Entity 2 polymer

Description description	HOLLIDAY JUNCTION DNA HELICASE RUVA
Molecular weight formula_weight	22111.7 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

MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL

Source Source

Source organism organism	Escherichia coli BL21(DE3)
NCBI taxonomy ID ncbi_taxonomy_id	469008
Host organism host_organism	Escherichia coli BL21(DE3)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1bdxa1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.1 — DNA helicase RuvA subunit, C-terminal domain
Family Family family	a.5.1.1 — DNA helicase RuvA subunit, C-terminal domain

Domain ID domain_id	d1bdxa2
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.2 — RuvA domain 2-like
Family Family family	a.60.2.1 — DNA helicase RuvA subunit, middle domain

Domain ID domain_id	d1bdxa3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

Domain ID domain_id	d1bdxb1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.1 — DNA helicase RuvA subunit, C-terminal domain
Family Family family	a.5.1.1 — DNA helicase RuvA subunit, C-terminal domain

Domain ID domain_id	d1bdxb2
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.2 — RuvA domain 2-like
Family Family family	a.60.2.1 — DNA helicase RuvA subunit, middle domain

Domain ID domain_id	d1bdxb3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

Domain ID domain_id	d1bdxc1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.1 — DNA helicase RuvA subunit, C-terminal domain
Family Family family	a.5.1.1 — DNA helicase RuvA subunit, C-terminal domain

Domain ID domain_id	d1bdxc2
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.2 — RuvA domain 2-like
Family Family family	a.60.2.1 — DNA helicase RuvA subunit, middle domain

Domain ID domain_id	d1bdxc3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

Domain ID domain_id	d1bdxd1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.1 — DNA helicase RuvA subunit, C-terminal domain
Family Family family	a.5.1.1 — DNA helicase RuvA subunit, C-terminal domain

Domain ID domain_id	d1bdxd2
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.2 — RuvA domain 2-like
Family Family family	a.60.2.1 — DNA helicase RuvA subunit, middle domain

Domain ID domain_id	d1bdxd3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

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Unit-cell length a length_a	148.000 Å
Unit-cell length b length_b	148.000 Å
Unit-cell length c length_c	105.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	6.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY

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

HOLLIDAY JUNCTION DNA HELICASE RUVA

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

1bdx__assembly_1__model_1

1bdx__assembly_1__model_1 | I(q)

1bdx__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (2)

E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY

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

HOLLIDAY JUNCTION DNA HELICASE RUVA

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

1bdx__assembly_1__model_1

1bdx__assembly_1__model_1 | I(q)

1bdx__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (2)