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7ujl

Bacteriophage Lambda Red-Beta N-terminal domain helical assembly in complex with dsDNA

Method: ELECTRON MICROSCOPY Dmax: 65.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Recombination protein bet

Escherichia virus Lambda

UniProt P03698

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 × 60 DNA 120 PDB declaration: 180-meric（180） Consistent with all polymer counts Chain A； UniProt 1–177 Fragment：N-terminal domain (UNP residues 1-177) Template DNA × 60 Complementary DNA × 60 ELECTRON MICROSCOPY cryo-EM buffer：pH 6 cryo-EM vitrification conditions：Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification. Resolution 3.30 Å
2 Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 1–177 Fragment：N-terminal domain (UNP residues 1-177) Template DNA × 1 Complementary DNA × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 6 cryo-EM vitrification conditions：Cryogen ETHANE；Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification. Resolution 3.30 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 7UJL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6M9K Crystal structure of lambda exonuclease in complex with the Red beta C-terminal domain Deposited 2018-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 194–260（67 aa）
Chain E 194–260（67 aa）
Chain F 194–260（67 aa）
Not recorded SO4 SULFATE ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；PEG3350, LISO4, BIS-TRIS
Resolution 2.30 Å R-free 0.254
8TFU Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1 Deposited 2023-07-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 182–261（80 aa）
Mutation：GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.48 M sodium phosphate monobasic monohydrate, 1.2 M potassium phosphate dibasic
Resolution 1.48 Å R-free 0.220
8TFU Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1 Deposited 2023-07-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 182–261（80 aa）
Mutation：GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.48 M sodium phosphate monobasic monohydrate, 1.2 M potassium phosphate dibasic
Resolution 1.48 Å R-free 0.220
8TG7 Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 2 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 182–261（80 aa）
Mutation：N-terminal GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298 K；2.0 M ammonium sulfate, 0.1 M Tris pH 8.6
Resolution 1.77 Å R-free 0.234
8TG7 Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 2 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 182–261（80 aa）
Mutation：N-terminal GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298 K；2.0 M ammonium sulfate, 0.1 M Tris pH 8.6
Resolution 1.77 Å R-free 0.234
8TG8 Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 3 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 182–261（80 aa）
Mutation：N-terminal GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298 K；1.2 M sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.6
Resolution 1.58 Å R-free 0.232
8TGC Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 4 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 182–261（80 aa）
Mutation：N-TERMINAL GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.4 M ammonium phosphate dibasic, 0.1M Tris pH 8.5
Resolution 1.48 Å R-free 0.259
8TGC Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 4 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 182–261（80 aa）
Mutation：N-TERMINAL GSHM No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.4 M ammonium phosphate dibasic, 0.1M Tris pH 8.5
Resolution 1.48 Å R-free 0.259

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VBET_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–177； UniProt 1–177

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 7ujl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ujl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ujl
Deposition date deposition_date2022-03-31
Structure title titleBacteriophage Lambda Red-Beta N-terminal domain helical assembly in complex with dsDNA
Keywords keywords;Annealase, Synaptase, SSAP, Single-strand annealing protein, DNA annealing intermediate, Recombinase, Two-component recombinase, Viral, DNA-binding, RECOMBINATION-DNA complex ;; RECOMBINATION/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.54 Å
Radius of gyration Rg (electron density) rg_electron18.81 Å
Forward intensity I(0) i09620600.00
Molecular weight molecular_weight20755.0 kDa
Excluded volume excluded_volume25083 ų
Envelope volume envelope_volume32602 ų
Hydration-shell volume shell_volume15295 ų
Envelope diameter envelope_diameter65.3 Å
Shell Rg shell_rg23.90 Å
Envelope Rg envelope_rg19.07 Å
Shape Rg shape_rg18.79 Å
Total Rg total_rg19.64 Å
Total atoms total_atoms1447
Residues n_residues169
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.5 Å
Rg (real space) rg_real19.55 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real9.6210e+06
I(0) uncertainty (real space) i0_real_error1.1750e+05
Rg (reciprocal space) rg_reciprocal19.55 Å
I(0) (reciprocal space) i0_reciprocal9621000.0000
Solution quality estimate total_estimate0.8893
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.6 Å
Skewness Skewness skewness0.330
Kurtosis Kurtosis kurtosis-0.407
Angular range angular_range— – 0.4050 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha1911000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)