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9y6v

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

Method: ELECTRON MICROSCOPY D_max: 178.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

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

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	47.07 Å
rg_electron	46.76 Å
i0	566603000.00
molecular_weight	173030.0 kDa
excluded_volume	207110 Å³
envelope_volume	315110 Å³
shell_volume	59091 Å³
envelope_diameter	181.1 Å
shell_rg	47.60 Å
envelope_rg	46.10 Å
shape_rg	46.69 Å
total_rg	46.97 Å
total_atoms	23114
n_residues	1296
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	178.7 Å
rg_real	47.48 Å
rg_real_error	2.51 Å
i0_real	5.6660e+08
i0_real_error	1.1080e+07
rg_reciprocal	47.07 Å
i0_reciprocal	566300000.0000
total_estimate	0.8220
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.1 Å
skewness	0.536
kurtosis	0.031
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	33070000.0000
n_real_points	34
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
formula_weight	71560.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	23114

MELKNIVNSYNITNILGYLRRSRQDMEREKRTGEDTLTEQKELMNKILTAIEIPYELKMEIGSGESIDGRPVFKECLKDLEEGKYQAIAVKEITRLSRGSYSDAGQIVNLLQSKRLIIITPYKVYDPRNPVDMRQIRFELFMAREEFEMTRERMTGAKYTYAAQGKWISGLAPYGYQLNKKTSKLDPVEDEAKVVQLIFNIFLNGLNGKDYSYTAIASHLTNLQIPTPSGKKRWNQYTIKAILQNEVYIGTVKYKVREKTKDGKRTIRPEKEQIVVQDAHAPIIDKEQFQQSQVKIANKVPLLPNKDEFELSELAGVCTCSKCGEPLSKYESKRIRKNKDGTESVYHVKSLTCKKNKCTYVRYNDVENAILDYLSSLNDLNDSTLTKHINSMLSKYEDDNSNMKTKKQMSEHLSQKEKELKNKENFIFDKYESGIYSDELFLKRKAALDEEFKELQNAKNELNGLQDTQSEIDSNTVRNNINKIIDQYHIESSSEKKNELLRMVLKDVIVNMTQKRKGPIPAQFEITPILRFNFIFDLTATNSFHTSGSGGSGGSGGSGRSGTEPYQRYEELKKKTIKVVQKENYSIRYITQDEASNDLDEFYKQFAQHLLEAALERKAE

Source

organism	Spbetavirus SPbeta
ncbi_taxonomy_id	66797
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	attPsym
formula_weight	20761.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

AAAAAAAAAAAGGTAGTAAGTATCTTAAAAAACAGATATAGCTGTATATTAAGATACTTACTACATA

Entity 3 polymer

description	attPsym
formula_weight	20528.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F

TATGTAGTAAGTATCTTAATATACAGCTATATCTGTTTTTTAAGATACTTACTACCTTTTTTTTTTT

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	7.10 Å
resolution_method	—
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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)