SAXSdb — 1d8l

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

PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)

Escherichia coli

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–149 Chain B； UniProt 1–149	Fragment：NH2 REGION	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；pH 4.60	Resolution 2.50 Å R-free 0.320

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 1D8L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BDX E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY Deposited 1998-05-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric	Chain A 1–203（203 aa） Chain B 1–203（203 aa） Chain C 1–203（203 aa） Chain D 1–203（203 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；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
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 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
1HJP HOLLIDAY JUNCTION BINDING PROTEIN RUVA FROM E. COLI Deposited 1997-08-21	Different construct Different mutation/modification 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149 Author chain B； PDBConstruct 1–149； UniProt 1–149

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	1d8l
Deposition date deposition_date	1999-10-25
Structure title title	E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING DOMAIN III
Keywords keywords	OB-FOLD, HELIX-HAIRPIN-HELIX MOTIF, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.92 Å
Radius of gyration Rg (electron density) rg_electron	21.98 Å
Forward intensity I(0) i0	15360500.00
Molecular weight molecular_weight	31161.0 kDa
Excluded volume excluded_volume	39794 Å³
Envelope volume envelope_volume	48587 Å³
Hydration-shell volume shell_volume	19232 Å³
Envelope diameter envelope_diameter	72.2 Å
Shell Rg shell_rg	27.75 Å
Envelope Rg envelope_rg	21.87 Å
Shape Rg shape_rg	21.97 Å
Total Rg total_rg	22.86 Å
Total atoms total_atoms	2192
Residues n_residues	280
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

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

Maximum dimension Dmax dmax	73.7 Å
Rg (real space) rg_real	22.92 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.5360e+07
I(0) uncertainty (real space) i0_real_error	2.3210e+05
Rg (reciprocal space) rg_reciprocal	22.92 Å
I(0) (reciprocal space) i0_reciprocal	15360000.0000
Solution quality estimate total_estimate	0.9001
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.291
Kurtosis Kurtosis kurtosis	-0.538
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5551000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d8la1
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	d1d8la2
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	d1d8lb1
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	d1d8lb2
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

CATH v4.4 (4 domains)

Domain ID domain_id	1d8lA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	1d8lA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1d8lB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	1d8lB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	79.600 Å
Unit-cell length b length_b	115.600 Å
Unit-cell length c length_c	34.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2470
R_work r_work	0.2430
R_free r_free	0.3200

Description description	PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)
Molecular weight formula_weight	16499.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2214

E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING DOMAIN III

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

PROTEIN (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

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

fit	/app/data/saxs_computation/d8/1d8l/1d8l.fit
pddf	/app/data/pr_computation/d8/1d8l/1d8l.pr.out
profile	/app/data/saxs_computation/d8/1d8l/1d8l.dat