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9v2m

Cryo-EM structure of KomBC Tetra-dimer

Method: ELECTRON MICROSCOPY D_max: 160.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v2m
deposition_date	2025-05-20
title	Cryo-EM structure of KomBC Tetra-dimer
keywords	KomB-KomC, dimer, 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	52.08 Å
rg_electron	51.56 Å
i0	2345520000.00
molecular_weight	408080.0 kDa
excluded_volume	512430 Å³
envelope_volume	705880 Å³
shell_volume	112850 Å³
envelope_diameter	168.3 Å
shell_rg	56.26 Å
envelope_rg	50.77 Å
shape_rg	51.52 Å
total_rg	51.84 Å
total_atoms	28792
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	160.5 Å
rg_real	51.92 Å
rg_real_error	1.02 Å
i0_real	2.3460e+09
i0_real_error	4.4360e+07
rg_reciprocal	52.20 Å
i0_reciprocal	2346000000.0000
total_estimate	0.8712
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.9 Å
skewness	0.218
kurtosis	-0.400
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	189500000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.539

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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	A,B,C,D,Q,R,S,T
atom_count	28792

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	E,F,G,H,U,V,W,X

MTTLTLSEAAPLLKKEFREGRLIPFLGAGFSKPLKLPDGSQLIASLAKTLGFEPELFDMHGRFEQLAEFFAISAPNRLQRLVYEMSLSFDSAEAEALREKSPMHRALAALDWRTIYTTNYDKHVEGALRDAGKQAAVLASFADFQGPRARDVCEVIKFHGTLDQPDTIVLTESSYFQRMALDAPPDQRLRADLLANSFLFIGYSFSDTNIRYIWYRMNQLREQSQLGVKHSQARRCFFATHGAGLVQPDILQQWNIDVIQLDPTDKSASVARLLESIA

Source

organism	Archangium gephyra
ncbi_taxonomy_id	48
host_organism	Escherichia coli

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6. Citations (1)

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resolution	3.67 Å
resolution_method	—
num_particles	119591

fit	/app/data/saxs_computation/v2/9v2m/9v2m.fit
pddf	/app/data/pr_computation/v2/9v2m/9v2m.pr.out
profile	/app/data/saxs_computation/v2/9v2m/9v2m.dat

Cryo-EM structure of KomBC Tetra-dimer

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)