SAXSdb — 8tg8

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

Recombination protein bet

Escherichia phage Lambda

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 182–261	Mutation：N-terminal GSHM	TRP-MET-ASP-PHE-ASP-ASP-ASP-ILE-PRO-PHE × 1	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

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 8TG8	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 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
7UJL Bacteriophage Lambda Red-Beta N-terminal domain helical assembly in complex with dsDNA Deposited 2022-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 60 PDB declaration: 180-meric	Chain A 1–177（177 aa） Fragment：N-terminal domain (UNP residues 1-177)	Not recorded	No recorded non-water small molecule	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
7UJL Bacteriophage Lambda Red-Beta N-terminal domain helical assembly in complex with dsDNA Deposited 2022-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–177（177 aa） Fragment：N-terminal domain (UNP residues 1-177)	Not recorded	No recorded non-water small molecule	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
8TFU Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1 Deposited 2023-07-11	Different mutation/modification 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 mutation/modification 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 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 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
8TGC Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 4 Deposited 2023-07-12	Different mutation/modification 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 mutation/modification 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 9 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 5–84； UniProt 182–261

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	8tg8
Deposition date deposition_date	2023-07-12
Structure title title	Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 3
Keywords keywords	;Recombination, Recombineering, Single Strand Annealing, Single-stranded DNA binding protein, genome engineering, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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	13.36 Å
Radius of gyration Rg (electron density) rg_electron	11.77 Å
Forward intensity I(0) i0	1631170.00
Molecular weight molecular_weight	8646.0 kDa
Excluded volume excluded_volume	10848 Å³
Envelope volume envelope_volume	12261 Å³
Hydration-shell volume shell_volume	9078 Å³
Envelope diameter envelope_diameter	40.5 Å
Shell Rg shell_rg	17.16 Å
Envelope Rg envelope_rg	12.15 Å
Shape Rg shape_rg	11.77 Å
Total Rg total_rg	13.16 Å
Total atoms total_atoms	608
Residues n_residues	77
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	41.9 Å
Rg (real space) rg_real	13.27 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.6310e+06
I(0) uncertainty (real space) i0_real_error	1.7290e+04
Rg (reciprocal space) rg_reciprocal	13.28 Å
I(0) (reciprocal space) i0_reciprocal	1631000.0000
Solution quality estimate total_estimate	0.8071
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.063
Kurtosis Kurtosis kurtosis	-0.353
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	256400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Recombination protein bet
Molecular weight formula_weight	9428.6 kDa
Mutation mutation	N-terminal GSHM
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	652

GSHMTAYTAERQPERDITPVNDETMQEINTLLIALDKTWDDDLLPLCSQIFRRDIRASSELTQAEAVKALGFLKQKAAEQKVAA

来源 Source

来源生物 organism	Escherichia phage Lambda
NCBI Class编号 ncbi_taxonomy_id	2681611
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	TRP-MET-ASP-PHE-ASP-ASP-ASP-ILE-PRO-PHE
Molecular weight formula_weight	1300.4 kDa
Mutation mutation	N-terminal Trp addded
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

WMDFDDDIPF

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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8. Citations (1)

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Unit-cell length a length_a	70.042 Å
Unit-cell length b length_b	70.042 Å
Unit-cell length c length_c	38.408 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.576 Å
Low-resolution limit resolution_low	49.527 Å
R factor r_factor	—
R_work r_work	0.2011
R_free r_free	0.2320

fit	/app/data/saxs_computation/tg/8tg8/8tg8.fit
pddf	/app/data/pr_computation/tg/8tg8/8tg8.pr.out
profile	/app/data/saxs_computation/tg/8tg8/8tg8.dat

Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 3

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

Recombination protein bet

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)