SAXSdb — 1bdx

▼

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Homooligomer Protein × 4 DNA 4 PDB declaration: octameric（8） Consistent with all polymer counts	Chain A； UniProt 1–203 Chain B； UniProt 1–203 Chain C； UniProt 1–203 Chain D； UniProt 1–203	Not recorded	;DNA (5'-D(PGPCPAPTPGPCPAPTPAPTPGPCPAPTPGPC)-3') ; × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；PROTEIN/DNA COMPLEX WAS CRYSTALLISED FROM 0.85M SODIUM ACETATE BUFFERED WITH 100MM IMIDAZOLE AT PH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 6.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1BDX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C7Y E.COLI RUVA-HOLLIDAY JUNCTION COMPLEX Deposited 2000-04-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: 36-meric	Chain A 1–203（203 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；ammonium sulfate, sodium chloride, glycerol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.279
1CUK ESCHERICHIA COLI RUVA PROTEIN AT PH 4.9 AND ROOM TEMPERATURE Deposited 1996-08-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–203（203 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1D8L E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING DOMAIN III Deposited 1999-10-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–149（149 aa） Fragment：NH2 REGION Chain B 1–149（149 aa） Fragment：NH2 REGION	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.60	Resolution 2.50 Å R-free 0.320
1HJP HOLLIDAY JUNCTION BINDING PROTEIN RUVA FROM E. COLI Deposited 1997-08-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–203（203 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.9；50MM CITRATE PH4.9 500MM NACL 10% GLYCEROL 3% PEG2000	Resolution 2.50 Å R-free 0.294

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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.

▼

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

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.56 Å
Radius of gyration Rg (electron density) rg_electron	29.40 Å
Forward intensity I(0) i0	121196000.00
Molecular weight molecular_weight	85549.0 kDa
Excluded volume excluded_volume	104190 Å³
Envelope volume envelope_volume	104850 Å³
Hydration-shell volume shell_volume	31820 Å³
Envelope diameter envelope_diameter	89.5 Å
Shell Rg shell_rg	34.85 Å
Envelope Rg envelope_rg	27.24 Å
Shape Rg shape_rg	29.61 Å
Total Rg total_rg	29.81 Å
Total atoms total_atoms	64
Residues n_residues	64
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	92.0 Å
Rg (real space) rg_real	30.39 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.2120e+08
I(0) uncertainty (real space) i0_real_error	1.5740e+06
Rg (reciprocal space) rg_reciprocal	30.47 Å
I(0) (reciprocal space) i0_reciprocal	121200000.0000
Solution quality estimate total_estimate	0.9137
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.1 Å
Skewness Skewness skewness	0.118
Kurtosis Kurtosis kurtosis	-0.605
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	14970000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.974

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. 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

来源 Source

来源生物 organism	Escherichia coli BL21(DE3)
NCBI Class编号 ncbi_taxonomy_id	469008
宿主生物 host_organism	Escherichia coli BL21(DE3)

▼

7. 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

▶

8. Citations (2)

▶

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	—

fit	/app/data/saxs_computation/bd/1bdx/1bdx.fit
pddf	/app/data/pr_computation/bd/1bdx/1bdx.pr.out
profile	/app/data/saxs_computation/bd/1bdx/1bdx.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)