← Back to search
1c7y

E.COLI RUVA-HOLLIDAY JUNCTION COMPLEX

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: GOOD
▼

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

HOLLIDAY JUNCTION DNA HELICASE RUVA

Escherichia coli

UniProt P0A809

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 32 PDB declaration: 36-meric（36） Consistent with all polymer counts Chain A； UniProt 1–203 Not recorded ;DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3') ; × 4 ;DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3') ; × 4 ;DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3') ; × 4 ;DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3') ; × 4 ;DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3') ; × 4 ;DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3') ; × 4 ;DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3') ; × 4 ;DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3') ; × 4 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

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 1C7Y 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
1CUK ESCHERICHIA COLI RUVA PROTEIN AT PH 4.9 AND ROOM TEMPERATURE Deposited 1996-08-28 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 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 9
Chains and sequence ranges Author chain A； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 1c7y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c7y
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1c7y
Deposition date deposition_date2000-04-03
Structure title titleE.COLI RUVA-HOLLIDAY JUNCTION COMPLEX
Keywords keywordshelix-hairpin-helix, protein-DNA complex, homologous recombination, Holliday junction, RECOMBINATION-DNA COMPLEX; RECOMBINATION/DNA
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier23.24 Å
Radius of gyration Rg (electron density) rg_electron22.00 Å
Forward intensity I(0) i020135700.00
Molecular weight molecular_weight29537.0 kDa
Excluded volume excluded_volume35118 ų
Envelope volume envelope_volume45558 ų
Hydration-shell volume shell_volume18732 ų
Envelope diameter envelope_diameter78.4 Å
Shell Rg shell_rg27.13 Å
Envelope Rg envelope_rg22.07 Å
Shape Rg shape_rg21.95 Å
Total Rg total_rg22.80 Å
Total atoms total_atoms2045
Residues n_residues224
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax78.8 Å
Rg (real space) rg_real23.29 Å
Rg uncertainty (real space) rg_real_error0.88 Å
I(0) (real space) i0_real2.0140e+07
I(0) uncertainty (real space) i0_real_error2.7870e+05
Rg (reciprocal space) rg_reciprocal23.28 Å
I(0) (reciprocal space) i0_reciprocal20140000.0000
Solution quality estimate total_estimate0.8818
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3 Å
Skewness Skewness skewness0.349
Kurtosis Kurtosis kurtosis-0.347
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1930000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.893; Smooth: 0.964
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (9)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1c7ya1
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.1 — DNA helicase RuvA subunit, C-terminal domain
Family Family familya.5.1.1 — DNA helicase RuvA subunit, C-terminal domain
Domain ID domain_idd1c7ya2
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.2 — RuvA domain 2-like
Family Family familya.60.2.1 — DNA helicase RuvA subunit, middle domain
Domain ID domain_idd1c7ya3
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id1c7yA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1c7yA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1c7yA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
▶

8. Citations (1)

▶

9. Files and Curves (10)