SAXSdb — 9ykx

▼

1. Structure Basics

entry_id	9ykx
deposition_date	2025-10-08
title	Un-crosslinked hClpX
keywords	Mitochondrial protein, serine protease, structural protein, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	43.48 Å
rg_electron	42.84 Å
i0	517649000.00
molecular_weight	192470.0 kDa
excluded_volume	243370 Å³
envelope_volume	374740 Å³
shell_volume	69506 Å³
envelope_diameter	139.9 Å
shell_rg	51.74 Å
envelope_rg	41.61 Å
shape_rg	42.88 Å
total_rg	43.15 Å
total_atoms	13558
n_residues	1829
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

▼

3. P(r) Analysis (GNOM)

dmax	135.9 Å
rg_real	43.29 Å
rg_real_error	1.06 Å
i0_real	5.1760e+08
i0_real_error	9.1570e+06
rg_reciprocal	43.48 Å
i0_reciprocal	517800000.0000
total_estimate	0.9034
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	64.2 Å
skewness	0.069
kurtosis	-0.719
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	419100000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.929

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	ATP-dependent clpX-like chaperone, mitochondrial
formula_weight	63569.0 kDa
ec_number	3.6.4.10
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	13558

FTETPAYFASKDGISKDGSGDGNKKSASEGSSKKSGSGNSGKGGNQLRCPKCGDLCTHVETFVSSTRFVKCEKCHHFFVVLSEADSKKSIIKEPESAAEAVKLAFQQKPPPPPKKIYNYLDKYVVGQSFAKKVLSVAVYNHYKRIYNNIPANLRQQAEVEKQTSLTPRELEIRRREDEYRFTKLLQIAGISPHGNALGASMQQQVNQQIPQEKRGGEVLDSSHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLLQDANYNVEKAQQGIVFLDEVDKIGSVPGIHQLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRKLRGETVQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTPSNLGKGRRAAAAADLANRSGESNTHQDIEEKDRLLRHVEARDLIEFGMIPEFVGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALERKTGARGLRSIMEKLLLEPMFEVPNSDIVCVEVDKEVVEGKKEPGYIRAPTKESSEEEYDSGVEEEGWPRQADAANS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

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	triclinic

resolution	4.40 Å
resolution_method	—
num_particles	46168

fit	/app/data/saxs_computation/yk/9ykx/9ykx.fit
pddf	/app/data/pr_computation/yk/9ykx/9ykx.pr.out
profile	/app/data/saxs_computation/yk/9ykx/9ykx.dat

Un-crosslinked hClpX

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

EM 3D