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

Method: ELECTRON MICROSCOPY D_max: 140.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9urj
deposition_date	2025-04-30
title	binary complex of polyP-bound polyphosphate kinase 1 (PPK1)
keywords	CryoEM, Transferase; TRANSFERASE
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	46.82 Å
rg_electron	45.73 Å
i0	1179900000.00
molecular_weight	292930.0 kDa
excluded_volume	370150 Å³
envelope_volume	533180 Å³
shell_volume	93030 Å³
envelope_diameter	144.2 Å
shell_rg	55.04 Å
envelope_rg	43.56 Å
shape_rg	45.73 Å
total_rg	46.11 Å
total_atoms	20676
n_residues	2496
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	140.5 Å
rg_real	46.38 Å
rg_real_error	0.78 Å
i0_real	1.1800e+09
i0_real_error	1.8390e+07
rg_reciprocal	46.81 Å
i0_reciprocal	1181000000.0000
total_estimate	0.8953
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.1 Å
skewness	-0.065
kurtosis	-0.586
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	112100000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.933

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Polyphosphate kinase
formula_weight	80013.8 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	20676

EKLYIEKELSWLSFNERVLQEAADKSNPLIERMRFLGIYSNNLDEFYKVRFAELKRRIIISEEQGSNSHSRHLLGKIQSRVLKADQEFDGLYNELLLEMARNQIFLINERQLSVNQQNWLRHYFKQYLRQHITPILINPDTDLVQFLKDDYTYLAVEIIRGDTIRYALLEIPSDKVPRFVNLPPEAPRRRKPMILLDNILRYCLDDIFKGFFDYDALNAYSMKMTRDAEYDLVHEMEASLMELMSSSLKQRLTAEPVRFVYQRDMPNALVEVLREKLTISRYDSIVPGGRYHNFKDFINFPNVGKANLVNKPLPRLRHIWFDKAQFRNGFDAIRERDVLLYYPYHTFEHVLELLRQASFDPSVLAIKINIYRVAKDSRIIDSMIHAAHNGKKVTVVVELQARFDEEANIHWAKRLTEAGVHVIFSAPGLKIHAKLFLISRKENGEVVRYAHIGTGNFNEKTARLYTDYSLLTADARITNEVRRVFNFIENPYRPVTFDYLMVSPQNSRRLLYEMVDREIANAQQGLPSGITLKLNNLVDKGLVDRLYAASSSGVPVNLLVAGMCSLIPNLEGISDNIRAISIVDRYLEHDRVYIFENGGDKKVYLSSADWMTRNIDYRIEVATPLLDPRLKQRVLDIIDILFSDTVKARYIDKELSNRYVPRGNRRKVRAQLAIYDYIKSLEQP

Source

organism	Escherichia coli (strain K12)
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	Tetraphosphate
formula_weight	337.9 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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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	—

resolution	3.11 Å
resolution_method	—
num_particles	38919

fit	/app/data/saxs_computation/ur/9urj/9urj.fit
pddf	/app/data/pr_computation/ur/9urj/9urj.pr.out
profile	/app/data/saxs_computation/ur/9urj/9urj.dat