binary complex of ATP-bound polyphosphate kinase 1 (PPK1)

Method: ELECTRON MICROSCOPY D_max: 139.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9uuh
deposition_date	2025-05-07
title	binary complex of ATP-bound polyphosphate kinase 1 (PPK1)
keywords	Cryo-EM, wild type PPK1, TRANSFERASE; TRANSFERASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	46.30 Å
rg_electron	45.23 Å
i0	1225390000.00
molecular_weight	297390.0 kDa
excluded_volume	375560 Å³
envelope_volume	535820 Å³
shell_volume	95319 Å³
envelope_diameter	142.5 Å
shell_rg	53.86 Å
envelope_rg	42.99 Å
shape_rg	45.23 Å
total_rg	45.59 Å
total_atoms	21000
n_residues	2528
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	139.4 Å
rg_real	45.88 Å
rg_real_error	0.67 Å
i0_real	1.2250e+09
i0_real_error	1.9330e+07
rg_reciprocal	46.30 Å
i0_reciprocal	1226000000.0000
total_estimate	0.8928
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	65.6 Å
skewness	-0.057
kurtosis	-0.572
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	149300000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.929

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Polyphosphate kinase
formula_weight	80015.7 kDa
ec_number	2.7.4.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	21000

KLYIEKELSWLAFNERVLQEAADKSNPLIERMRFLGIYSNNLDEFYKVRFAELKRRIIISEEQGSNSHSRHLLGKIQARVLKADQEFDGLYNELLLEMARNQIFLINERQLSANQQSWLRHYFKQYLRQHITPILINRETDLVQFLKDDYTYLAVEIIRGDTIRYALLEIPSDKVPRFVNLPPETPRRRKPMILLDNILRYCLDDIFKGFFDYDALNAYSMKMTRDAEYDLVHEMESSLMELMSSSLKQRLTAEPVRFVYQRDMPNALVEVLREKLTISRYDSIVPGGRYHNFKDFINFPNVGKANLVNKPLPRLRHIWFDNEKFRNGFDAIRERDVLLYYPYHTFEHVLELLRQASFDPSVLAIKINIYRVAKDSRIIDAMIHAAHNSKKVTVVVELQARFDEEANIHWAKRLTEAGVHVIFSAPGLKIHAKLFLISRKEGDEVVRYAHIGTGNFNEKTARLYTDYSLLTADSRITNEVRRVFNFIENPYRPVTFDYLLVSPQNSRRLLYAMIDKEIANAQQGQPSGITLKLNNLVDKGLVDRLYAASSSGVPVNLLIRGMCSLIPNLEGISDNIRVISIVDRYLEHDRVYIFENGGDKQVYLSSADWMTRNIDYRIEVATPLLDPRLKQRVLDIIDILFSDTVKARFIDKELSNRYVPRGNRRKVQSQLAIYDYIKSLEQP

Source

organism	Citrobacter freundii
ncbi_taxonomy_id	546
host_organism	Escherichia coli

Entity 2 non-polymer

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

▶

6. Citations (1)

▶

resolution	3.07 Å
resolution_method	—
num_particles	55294

fit	/app/data/saxs_computation/uu/9uuh/9uuh.fit
pddf	/app/data/pr_computation/uu/9uuh/9uuh.pr.out
profile	/app/data/saxs_computation/uu/9uuh/9uuh.dat