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9xvc

Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments

Method: ELECTRON MICROSCOPY D_max: 173.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xvc
deposition_date	2025-11-26
title	Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
keywords	KomBC, NAD hydrolysis protein, IMMUNE SYSTEM; IMMUNE SYSTEM
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	53.38 Å
rg_electron	52.51 Å
i0	2348260000.00
molecular_weight	416870.0 kDa
excluded_volume	526100 Å³
envelope_volume	715990 Å³
shell_volume	112930 Å³
envelope_diameter	172.1 Å
shell_rg	56.53 Å
envelope_rg	51.86 Å
shape_rg	52.48 Å
total_rg	52.76 Å
total_atoms	29400
n_residues	3568
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	173.5 Å
rg_real	53.22 Å
rg_real_error	1.70 Å
i0_real	2.3480e+09
i0_real_error	4.1520e+07
rg_reciprocal	53.49 Å
i0_reciprocal	2349000000.0000
total_estimate	0.8688
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.8 Å
skewness	0.213
kurtosis	-0.403
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	187100000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.670

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
formula_weight	20929.1 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	C,D,A,B,K,L,I,J
atom_count	29400

MNIRFITRNRHKIKEINKILSGTGVVVLASEHSIDEIQTENVHALIKDKLLKAFKLVGRPVFVEHTGLYIESLNGFPGGLTQIFWDKLQADKFSQLLGTSENPRLVAKTIIGYCDSMKIYIFEGETQGTISPVPKGPRDFQWDCIFIPDGESETFAEMGDRKNEISMRKKAFDKFKEYLLEGGK

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	KomC(H146N), a SIR2-domain NADase
formula_weight	30631.8 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	H,G,F,E,P,O,N,M

MEQLLADYKKGNVILFVGAGVSMNLGLPSWSQLVDHIATELGYDPDIYRTFGSALELAEYYKLKKGKIGPLRSWMDRMWHSSDIDINKSKVHEYIAKANFPIIYTTNYDRWIETALSNYGKEYIKISSVSDIAKIDNNKTQIIKFNGDFDDDSSIVLDETSYFQRLEFETPLDIKFRSDVLGKSVLFIGYSLSDINIRLLFYKLSKLWKEQKLEEAQPKSYIFLPRPNPIQEEILEQWRIGMISSENDNPGESLEEFLKNFVLV

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
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	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	8

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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	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	208086

fit	/app/data/saxs_computation/xv/9xvc/9xvc.fit
pddf	/app/data/pr_computation/xv/9xvc/9xvc.pr.out
profile	/app/data/saxs_computation/xv/9xvc/9xvc.dat

Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments

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

Refinement

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)