SAXSdb — 9y6v

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

Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN

Spbetavirus SPbeta

UniProt O32006

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 1–545 Chain B； UniProt 1–545 Chain C； UniProt 1–545 Chain D； UniProt 1–545	Not recorded	attPsym × 1 attPsym × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20mM Tris-HCl, 100mM NaCl cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 7.10 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 9Y6V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9DXD attLmm bound serine integrase and RDF complex in the pre-rotation state Deposited 2024-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: 16-meric	Chain A 1–545（545 aa） Chain B 1–545（545 aa） Chain C 1–545（545 aa） Chain D 1–545（545 aa） Chain I 1–545（545 aa） Chain J 1–545（545 aa） Chain K 1–545（545 aa） Chain L 1–545（545 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.16 Å
9DXF attLmm bound serine integrase and RDF complex in the post-rotation state Deposited 2024-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: 16-meric	Chain A 1–545（545 aa） Chain B 1–545（545 aa） Chain C 1–545（545 aa） Chain D 1–545（545 aa） Chain I 1–545（545 aa） Chain J 1–545（545 aa） Chain K 1–545（545 aa） Chain L 1–545（545 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.16 Å
9DXG attP bound large serine integrase and RDF complex in the dimeric state (cleaved) Deposited 2024-10-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: octameric	Chain A 1–545（545 aa） Chain B 1–545（545 aa） Chain C 1–545（545 aa） Chain D 1–545（545 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.61 Å
9DXH attPmm and attBmm bound serine integrase complex in the pre-rotation state Deposited 2024-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: 12-meric	Chain A 1–545（545 aa） Chain C 1–545（545 aa） Chain I 1–545（545 aa） Chain K 1–545（545 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.69 Å
9DXJ attPmm and attBmm bound serine integrase complex in the post-rotation state Deposited 2024-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: 12-meric	Chain A 1–545（545 aa） Chain C 1–545（545 aa） Chain I 1–545（545 aa） Chain K 1–545（545 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.69 Å
9DXK attPmm bound serine integrase complex in the tetrameric state Deposited 2024-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: 12-meric	Chain A 1–545（545 aa） Chain C 1–545（545 aa） Chain I 1–545（545 aa） Chain K 1–545（545 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.81 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YOKA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–545； UniProt 1–545 Author chain B； PDBConstruct 1–545； UniProt 1–545 Author chain C； PDBConstruct 1–545； UniProt 1–545 Author chain D； PDBConstruct 1–545； UniProt 1–545

Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN

Spbetavirus SPbeta

UniProt O34850

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 2–58 Chain B； UniProt 2–58 Chain C； UniProt 2–58 Chain D； UniProt 2–58	Not recorded	attPsym × 1 attPsym × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20mM Tris-HCl, 100mM NaCl cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 7.10 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 9Y6V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9DXD attLmm bound serine integrase and RDF complex in the pre-rotation state Deposited 2024-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: 16-meric	Chain A 2–58（57 aa） Chain B 2–58（57 aa） Chain C 2–58（57 aa） Chain D 2–58（57 aa） Chain I 2–58（57 aa） Chain J 2–58（57 aa） Chain K 2–58（57 aa） Chain L 2–58（57 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.16 Å
9DXF attLmm bound serine integrase and RDF complex in the post-rotation state Deposited 2024-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: 16-meric	Chain A 2–58（57 aa） Chain B 2–58（57 aa） Chain C 2–58（57 aa） Chain D 2–58（57 aa） Chain I 2–58（57 aa） Chain J 2–58（57 aa） Chain K 2–58（57 aa） Chain L 2–58（57 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.16 Å
9DXG attP bound large serine integrase and RDF complex in the dimeric state (cleaved) Deposited 2024-10-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: octameric	Chain A 2–58（57 aa） Chain B 2–58（57 aa） Chain C 2–58（57 aa） Chain D 2–58（57 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.61 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YOTN_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 564–620； UniProt 2–58 Author chain B； PDBConstruct 564–620； UniProt 2–58 Author chain C； PDBConstruct 564–620； UniProt 2–58 Author chain D； PDBConstruct 564–620； UniProt 2–58

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	9y6v
Deposition date deposition_date	2025-09-09
Structure title title	attPsym bound large serine integrase and RDF complex in the dimeric state
Keywords keywords	;Site-specific DNA Recombinase, Large serine integrase, DNA binding domains, Recombinase, Resolvase, Zinc ribbon recombinase, RECOMBINATION ;; RECOMBINATION
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	47.07 Å
Radius of gyration Rg (electron density) rg_electron	46.76 Å
Forward intensity I(0) i0	566603000.00
Molecular weight molecular_weight	173030.0 kDa
Excluded volume excluded_volume	207110 Å³
Envelope volume envelope_volume	315110 Å³
Hydration-shell volume shell_volume	59091 Å³
Envelope diameter envelope_diameter	181.1 Å
Shell Rg shell_rg	47.60 Å
Envelope Rg envelope_rg	46.10 Å
Shape Rg shape_rg	46.69 Å
Total Rg total_rg	46.97 Å
Total atoms total_atoms	23114
Residues n_residues	1296
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	178.7 Å
Rg (real space) rg_real	47.48 Å
Rg uncertainty (real space) rg_real_error	2.51 Å
I(0) (real space) i0_real	5.6660e+08
I(0) uncertainty (real space) i0_real_error	1.1080e+07
Rg (reciprocal space) rg_reciprocal	47.07 Å
I(0) (reciprocal space) i0_reciprocal	566300000.0000
Solution quality estimate total_estimate	0.8220
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.1 Å
Skewness Skewness skewness	0.536
Kurtosis Kurtosis kurtosis	0.031
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33070000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.652; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.842; Smooth: 0.883

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
Molecular weight formula_weight	71560.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	23114

MELKNIVNSYNITNILGYLRRSRQDMEREKRTGEDTLTEQKELMNKILTAIEIPYELKMEIGSGESIDGRPVFKECLKDLEEGKYQAIAVKEITRLSRGSYSDAGQIVNLLQSKRLIIITPYKVYDPRNPVDMRQIRFELFMAREEFEMTRERMTGAKYTYAAQGKWISGLAPYGYQLNKKTSKLDPVEDEAKVVQLIFNIFLNGLNGKDYSYTAIASHLTNLQIPTPSGKKRWNQYTIKAILQNEVYIGTVKYKVREKTKDGKRTIRPEKEQIVVQDAHAPIIDKEQFQQSQVKIANKVPLLPNKDEFELSELAGVCTCSKCGEPLSKYESKRIRKNKDGTESVYHVKSLTCKKNKCTYVRYNDVENAILDYLSSLNDLNDSTLTKHINSMLSKYEDDNSNMKTKKQMSEHLSQKEKELKNKENFIFDKYESGIYSDELFLKRKAALDEEFKELQNAKNELNGLQDTQSEIDSNTVRNNINKIIDQYHIESSSEKKNELLRMVLKDVIVNMTQKRKGPIPAQFEITPILRFNFIFDLTATNSFHTSGSGGSGGSGGSGRSGTEPYQRYEELKKKTIKVVQKENYSIRYITQDEASNDLDEFYKQFAQHLLEAALERKAE

来源 Source

来源生物 organism	Spbetavirus SPbeta
NCBI Class编号 ncbi_taxonomy_id	66797
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	attPsym
Molecular weight formula_weight	20761.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

AAAAAAAAAAAGGTAGTAAGTATCTTAAAAAACAGATATAGCTGTATATTAAGATACTTACTACATA

Entity 3 Entity 3 polymer

Description description	attPsym
Molecular weight formula_weight	20528.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

TATGTAGTAAGTATCTTAATATACAGCTATATCTGTTTTTTAAGATACTTACTACCTTTTTTTTTTT

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	7.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	24616

fit	/app/data/saxs_computation/y6/9y6v/9y6v.fit
pddf	/app/data/pr_computation/y6/9y6v/9y6v.pr.out
profile	/app/data/saxs_computation/y6/9y6v/9y6v.dat

attPsym bound large serine integrase and RDF complex in the dimeric state

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

Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN

State in the Current Structure

Other States of the Same Protein in the Database

Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)