SAXSdb — 8tfu

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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：GSHM	Plasmid-derived single-stranded DNA-binding protein × 1 （P28044）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 182–261	Mutation：GSHM	Plasmid-derived single-stranded DNA-binding protein × 1 （P28044）	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

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 8TFU	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
8TG7 Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 2 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 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 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：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 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：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 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 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 5–84； UniProt 182–261 Author chain B； PDBConstruct 5–84； UniProt 182–261

Plasmid-derived single-stranded DNA-binding protein

OrganismNot specified

UniProt P28044

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 D； UniProt 166–175	Fragment：C-terminal peptide	Recombination protein bet × 1 （P03698）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 166–175	Fragment：C-terminal peptide	Recombination protein bet × 1 （P03698）	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

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 8TFU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8TG7 Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 2 Deposited 2023-07-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 166–175（10 aa）	Not recorded	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 experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 166–175（10 aa）	Not recorded	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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 166–175（10 aa） Fragment：C-terminal peptide	Not recorded	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 experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 166–175（10 aa） Fragment：C-terminal peptide	Not recorded	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

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

View Construct and Data Evidence

UniProt name	SSB7_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 166–175 Author chain D； PDBConstruct 1–10； UniProt 166–175

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	8tfu
Deposition date deposition_date	2023-07-11
Structure title title	Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1
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	18.32 Å
Radius of gyration Rg (electron density) rg_electron	17.33 Å
Forward intensity I(0) i0	6049370.00
Molecular weight molecular_weight	17894.0 kDa
Excluded volume excluded_volume	22394 Å³
Envelope volume envelope_volume	27279 Å³
Hydration-shell volume shell_volume	13929 Å³
Envelope diameter envelope_diameter	59.8 Å
Shell Rg shell_rg	22.37 Å
Envelope Rg envelope_rg	17.51 Å
Shape Rg shape_rg	17.31 Å
Total Rg total_rg	18.29 Å
Total atoms total_atoms	1258
Residues n_residues	159
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	61.3 Å
Rg (real space) rg_real	18.32 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	6.0490e+06
I(0) uncertainty (real space) i0_real_error	7.9290e+04
Rg (reciprocal space) rg_reciprocal	18.32 Å
I(0) (reciprocal space) i0_reciprocal	6049000.0000
Solution quality estimate total_estimate	0.8737
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.9 Å
Skewness Skewness skewness	0.336
Kurtosis Kurtosis kurtosis	-0.409
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1460000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.991

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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	GSHM
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1407

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	Plasmid-derived single-stranded DNA-binding protein
Molecular weight formula_weight	1300.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

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	149

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8. Citations (1)

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Unit-cell length a length_a	37.810 Å
Unit-cell length b length_b	68.252 Å
Unit-cell length c length_c	70.888 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.482 Å
Low-resolution limit resolution_low	34.149 Å
R factor r_factor	—
R_work r_work	0.1815
R_free r_free	0.2202

fit	/app/data/saxs_computation/tf/8tfu/8tfu.fit
pddf	/app/data/pr_computation/tf/8tfu/8tfu.pr.out
profile	/app/data/saxs_computation/tf/8tfu/8tfu.dat

Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1

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

Plasmid-derived single-stranded DNA-binding protein

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)