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9v0z

Cryo-EM structure of KomBC Tetramer

Method: ELECTRON MICROSCOPY D_max: 158.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v0z
deposition_date	2025-05-19
title	Cryo-EM structure of KomBC Tetramer
keywords	Cryo-EM structure of KomB-KomC Oligomer, 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	45.46 Å
rg_electron	45.71 Å
i0	607739000.00
molecular_weight	204210.0 kDa
excluded_volume	256560 Å³
envelope_volume	341000 Å³
shell_volume	66132 Å³
envelope_diameter	167.7 Å
shell_rg	46.19 Å
envelope_rg	45.46 Å
shape_rg	45.66 Å
total_rg	45.88 Å
total_atoms	14408
n_residues	1828
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	158.2 Å
rg_real	45.97 Å
rg_real_error	1.84 Å
i0_real	6.0770e+08
i0_real_error	1.3300e+07
rg_reciprocal	45.46 Å
i0_reciprocal	607400000.0000
total_estimate	0.7883
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.7 Å
skewness	0.706
kurtosis	0.221
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	56340000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.665; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.353

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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	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14408

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	4

Polymer

type	polypeptide(L)
strand_id	E,F,G,H

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	2.35 Å
resolution_method	—
num_particles	213475

fit	/app/data/saxs_computation/v0/9v0z/9v0z.fit
pddf	/app/data/pr_computation/v0/9v0z/9v0z.pr.out
profile	/app/data/saxs_computation/v0/9v0z/9v0z.dat

Cryo-EM structure of KomBC 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)