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9v2k

Cryo-EM structure of KomBC Tetra-tetramer

Method: ELECTRON MICROSCOPY D_max: 247.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v2k
deposition_date	2025-05-20
title	Cryo-EM structure of KomBC Tetra-tetramer
keywords	Cryo-EM, KomB-KomC, 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	70.23 Å
rg_electron	70.04 Å
i0	9107990000.00
molecular_weight	816170.0 kDa
excluded_volume	1024900 Å³
envelope_volume	1533400 Å³
shell_volume	179390 Å³
envelope_diameter	231.0 Å
shell_rg	70.57 Å
envelope_rg	68.91 Å
shape_rg	70.01 Å
total_rg	70.14 Å
total_atoms	57584
n_residues	7312
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	247.5 Å
rg_real	73.52 Å
rg_real_error	1.30 Å
i0_real	9.1370e+09
i0_real_error	1.7560e+08
rg_reciprocal	70.21 Å
i0_reciprocal	9107000000.0000
total_estimate	0.8973
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	78.7 Å
skewness	0.516
kurtosis	-0.073
angular_range	— – 0.1100 Å⁻¹
current_alpha	1.1110
highest_alpha	3190000000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 0.881; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.677

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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	16

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,I,J,K,L,Q,R,S,T,Y,Z,a,b
atom_count	57584

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	16

Polymer

type	polypeptide(L)
strand_id	E,F,G,H,M,N,O,P,U,V,W,X,c,d,e,f

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	3.50 Å
resolution_method	—
num_particles	328747

fit	/app/data/saxs_computation/v2/9v2k/9v2k.fit
pddf	/app/data/pr_computation/v2/9v2k/9v2k.pr.out
profile	/app/data/saxs_computation/v2/9v2k/9v2k.dat

Cryo-EM structure of KomBC Tetra-tetramer

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)