SAXSdb — 9ten

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1. Structure Basics

entry_id	9ten
deposition_date	2025-11-25
title	PhiC31 excisive synapse: B-bound subregion
keywords	Serine integrase, Recombinase, Site-specific recombination, RDF, DNA, 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	34.03 Å
rg_electron	34.26 Å
i0	148527000.00
molecular_weight	84974.0 kDa
excluded_volume	100930 Å³
envelope_volume	138770 Å³
shell_volume	35256 Å³
envelope_diameter	121.8 Å
shell_rg	38.83 Å
envelope_rg	34.20 Å
shape_rg	34.28 Å
total_rg	34.53 Å
total_atoms	5906
n_residues	662
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	115.9 Å
rg_real	34.14 Å
rg_real_error	1.08 Å
i0_real	1.4850e+08
i0_real_error	2.9660e+06
rg_reciprocal	34.07 Å
i0_reciprocal	148500000.0000
total_estimate	0.8714
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	32.0 Å
skewness	0.378
kurtosis	-0.461
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	13750000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.808; Smooth: 0.920

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	attL60_Fw
formula_weight	18701.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E
atom_count	5906

AGCCGCGGTGCGGGTGCCAGGGCGTGCCCTTGAGTTCTCTCAGTTGGGGGCGTAGGGTCG

Entity 2 polymer

description	attL60_Rv
formula_weight	18293.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F

CGACCCTACGCCCCCAACTGAGAGAACTCAAGGGCACGCCCTGGCACCCGCACCGCGGCT

Entity 3 polymer

description	Recombination directionality factor
formula_weight	30669.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MSYYHHHHHHDYDIPTTENLYFQGAMAMAKRSIWAGDEDNKPKKRETYADDTVGRFHSGYSETNERGKVVPVALDKWRISTGEQSVADAVAQLFGGTPVENEESTSENFIDVFTDRPKVPVIIEADGIHWDMKLWLNGKLKHHCDGFDFVSHADEEMIGQPCGCPKLFDERKAAAKEYDAPNPAITVTFTLADDPELGRFKFQTGSWTLFKVLHEAEDDVERVGKGGAVLANLELELVEYTPKRGPMRNKLVSYYKPTITVLKSYNDAIAD

Source

organism	Lomovskayavirus C31
ncbi_taxonomy_id	10719
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	Integrase
formula_weight	69566.4 kDa
mutation	S12A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGSSHHHHHHSSGLVPRGSHMDTYAGAYDRQARERENSSAASPATQRSANEDKAADLQREVERDGGRFRFVGHFSEAPGTSAFGTAERPEFERILNECRAGRLNMIIVYDVSRFSRLKVMDAIPIVSELLALGVTIVSTQEGVFRQGNVMDLIHLIMRLDASHKESSLKSAKILDTKNLQRELGGYVGGKAPYGFELVSETKEITRNGRMVNVVINKLAHSTTPLTGPFEFEPDVIRWWWREIKTHKHLPFKPGSQAAIHPGSITGLCKRMDADAVPTRGETIGKKTASSAWDPATVMRILRDPRIAGFAAEVIYKKKPDGTPTTKIEGYRIQRDPITLRPVELDCGPIIEPAEWYELQAWLDGRGRGKGLSRGQAILSAMDKLYCECGAVMTSKRGEESIKDSYRCRRRKVVDPSAPGQHEGTCNVSMAALDKFVAERIFNKIRHAEGDEETLALLWEAARRFGKLTEAPEKSGERANLVAERADALNALEELYEDRAAGAYDGPVGRKHFRKQQAALTLRQQGAEERLAELEAAEAPKLPLDQWFPEDADADPTGPKSWWGRASVDDKRVFVGLFVDKIVVTKSTTGRGQGTPIEKRASITWAKPPTDDDEDDAQDGTEDVAATS

Source

organism	Lomovskayavirus C31
ncbi_taxonomy_id	10719
host_organism	Escherichia coli BL21(DE3)

Entity 5 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	triclinic

resolution	3.11 Å
resolution_method	—
num_particles	115490

fit	/app/data/saxs_computation/te/9ten/9ten.fit
pddf	/app/data/pr_computation/te/9ten/9ten.pr.out
profile	/app/data/saxs_computation/te/9ten/9ten.dat

PhiC31 excisive synapse: B-bound subregion

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)