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9v57

Helical structure of KomBC in complex with dITP

Method: ELECTRON MICROSCOPY D_max: 168.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v57
deposition_date	2025-05-25
title	Helical structure of KomBC in complex with dITP
keywords	KomBc, dITP, Sir2, CELL INVASION; CELL INVASION
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	52.65 Å
rg_electron	52.02 Å
i0	2442930000.00
molecular_weight	412420.0 kDa
excluded_volume	516000 Å³
envelope_volume	701350 Å³
shell_volume	111720 Å³
envelope_diameter	169.8 Å
shell_rg	56.44 Å
envelope_rg	51.05 Å
shape_rg	51.97 Å
total_rg	52.32 Å
total_atoms	29032
n_residues	3656
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	168.3 Å
rg_real	52.48 Å
rg_real_error	1.26 Å
i0_real	2.4430e+09
i0_real_error	4.3890e+07
rg_reciprocal	52.78 Å
i0_reciprocal	2444000000.0000
total_estimate	0.8221
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.7 Å
skewness	0.198
kurtosis	-0.414
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	168700000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Xanthosine/inosine triphosphate pyrophosphatase
formula_weight	20012.0 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	C,F,I,L,a,d,o,r
atom_count	29032

MAPTWFYNTTNSEKLRELQHVLGGSAKLGYLTAKVTEILDVDLETVIRAKAIAAYRAVRVPVIVEHGALCIDALNGLPGALVKPFWESLDTRLCEVIPAGQRTARARGALCYCDGRERHVLIEETEGEIAPSARGTGGFHWDPIFIPKGQTRTFAEMSLDEKLSFSPLGRLHTRLRTELGL

Source

organism	Archangium gephyra
ncbi_taxonomy_id	48
host_organism	Escherichia coli

Entity 2 polymer

description	NAD-dependent protein deacetylase
formula_weight	31370.7 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	g,h,i,j,s,t,u,v

MTTLTLSEAAPLLKKEFREGRLIPFLGAGFSKPLKLPDGSQLIASLAKTLGFEPELFDMHGRFEQLAEFFAISAPNRLQRLVYEMSLSFDSAEAEALREKSPMHRALAALDWRTIYTTNYDKHVEGALRDAGKQAAVLASFADFQGPRARDVCEVIKFHGTLDQPDTIVLTESSYFQRMALDAPPDQRLRADLLANSFLFIGYSFSDTNIRYIWYRMNQLREQSQLGVKHSQARRCFFATHGAGLVQPDILQQWNIDVIQLDPTDKSASVARLLESIA

Source

organism	Archangium gephyra
ncbi_taxonomy_id	48
host_organism	Escherichia coli

Entity 3 non-polymer

description	;2'-deoxyinosine 5'-triphosphate ;
formula_weight	492.2 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	8

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6. Citations (1)

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resolution	3.04 Å
resolution_method	—
num_particles	1574792

fit	/app/data/saxs_computation/v5/9v57/9v57.fit
pddf	/app/data/pr_computation/v5/9v57/9v57.pr.out
profile	/app/data/saxs_computation/v5/9v57/9v57.dat

Helical structure of KomBC in complex with dITP

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)