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9v12

Helical structure of KomBCMUT in complex with dITP and NAD

Method: ELECTRON MICROSCOPY D_max: 167.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v12
deposition_date	2025-05-19
title	Helical structure of KomBCMUT in complex with dITP and NAD
keywords	Cryo-EM, 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	52.62 Å
rg_electron	52.05 Å
i0	2527030000.00
molecular_weight	416860.0 kDa
excluded_volume	520350 Å³
envelope_volume	704160 Å³
shell_volume	111840 Å³
envelope_diameter	169.7 Å
shell_rg	56.55 Å
envelope_rg	51.22 Å
shape_rg	52.01 Å
total_rg	52.33 Å
total_atoms	29320
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	167.2 Å
rg_real	52.45 Å
rg_real_error	1.10 Å
i0_real	2.5270e+09
i0_real_error	4.9950e+07
rg_reciprocal	52.74 Å
i0_reciprocal	2528000000.0000
total_estimate	0.8757
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.3 Å
skewness	0.197
kurtosis	-0.414
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	167300000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.675

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	I,K,M,O,R,T,V,X
atom_count	29320

MAPTWFYNTTNSEKLRELQHVLGGSAKLGYLTAKVTEILDVDLETVIRAKAIAAYRAVRVPVIVEHGALCIDALNGLPGALVKPFWESLDTRLCEVIPAGQRTARARGALCYCDGRERHVLIEETEGEIAPSARGTGGFHWDPIFIPKGQTRTFAEMSLDEKLSFSPLGRLHTRLRTELGL

Source

organism	Archangium gephyra
ncbi_taxonomy_id	48
host_organism	Escherichia coli

Entity 2 polymer

description	NAD-dependent protein deacetylase
formula_weight	31260.6 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	i,j,k,l,m,n,o,p

MTTLTLSEAAPLLKKEFREGRLIPFLGAGFSKPLKLPDGSQLIASLAKTLGFEPELFDMHGRFEQLAEFFAISAPNRLQRLVYEMSLSFDSAEAEALREKSPMHRALAALDWRTIYTTAYDKHVEGALRDAGKQAAVLASFADFQGPRARDVCEVIKFAGTLDQPDTIVLTESSYFQRMALDAPPDQRLRADLLANSFLFIGYSFSDTNIRYIWYRMNQLREQSQLGVKHSQARRCFFATHGAGLVQPDILQQWNIDVIQLDPTDKSASVARLLESIA

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

Entity 5 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	8

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6. Citations (1)

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resolution	2.57 Å
resolution_method	—
num_particles	597778

fit	/app/data/saxs_computation/v1/9v12/9v12.fit
pddf	/app/data/pr_computation/v1/9v12/9v12.pr.out
profile	/app/data/saxs_computation/v1/9v12/9v12.dat

Helical structure of KomBCMUT in complex with dITP and NAD

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)