Glycogen phosphorylase from Segatella copri pentamer in complex with AMP chains D and E

Method: ELECTRON MICROSCOPY D_max: 167.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u3k
deposition_date	2025-03-18
title	Glycogen phosphorylase from Segatella copri pentamer in complex with AMP chains D and E
keywords	glycogen metabolism, cryo-EM, gut bacteria, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	46.96 Å
rg_electron	47.22 Å
i0	571814000.00
molecular_weight	198720.0 kDa
excluded_volume	248440 Å³
envelope_volume	339680 Å³
shell_volume	59917 Å³
envelope_diameter	176.0 Å
shell_rg	51.12 Å
envelope_rg	47.42 Å
shape_rg	47.18 Å
total_rg	47.49 Å
total_atoms	14006
n_residues	1702
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	167.3 Å
rg_real	47.37 Å
rg_real_error	1.80 Å
i0_real	5.7180e+08
i0_real_error	1.2280e+07
rg_reciprocal	46.97 Å
i0_reciprocal	571500000.0000
total_estimate	0.8416
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.4 Å
skewness	0.494
kurtosis	-0.290
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	93210000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.818

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Alpha-glucan family phosphorylase
formula_weight	98795.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,E
atom_count	14006

MKIKADYANAPQWKETTIKSSLPKELKCLDEIAHNMWWAWNYEGRDLFKSLDPDLYEKCNANPVLLLERLSYDRKEAIVKDKETMAKVKNVYKMFREYMDVKPNAKRPSVAYFCMEYGINQVVKIYSGGLGMLAGDYLKEASDSNVDMCAVGFLYRYGYFKQSLSMDGQQIANYDAQNFNSLPIERVYDENGNPLVVDVPYTNYQVHAYVWQMNVGRIKLYLLDTDNDMNSEFDRPITYSLYGGDWENRLKQEILLGIGGILTLKKLGIKKEIYHCNEGHAALCNLQRLCDYIEEDGLNFNQALELVRASSLYTVHTPVPAGHDYFDEALFGKYMGGYPQRLGISWDEFIGMGRENADDHNERFCLSTFACNTCQEVNGVSKLHGWVSQQMFSNIWKGYFPEENHVGYVTNGVHFPTWTATEWRKLYDTYFDKNFMNDQSNEEIWHAIYKVSDAEIWNTRMTLKKKLVAYIREKFTQTWLKNQGDPARVVSLLERINPNALMIGFCRRFATYKRAHLLFTDLERLSKIVNDPEHPVLFFFSGKAHPADGAGQGLIKKIFEISQRPEFLGKIIFLEDYDMTLARRLVSGVDIWMNTPTRPLEASGTSGEKAEMNGVVNLSVLDGWWVEGYREGAGWALPEKRTYQNQGYQDQLDAATIYNLLENDIIPMYYNKNKEGFSKEWIQVVKNSIATIAPHYTMKRQLDDYYDKFYNKEAARFKKLSANDNALAKEIALWKESVAERWDGIHVVSKDDCMLMAAETGQKIKVQYVIDEQGLNDAVGLELVVLKEQPEDGKQVYAVYPFKMVGHEGNNFTFEAEIEPINAGSFKTGVRMYPKNDKLPHRQDFCYVKWLN

Source

organism	Segatella copri
ncbi_taxonomy_id	165179
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 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	3.32 Å
resolution_method	—
num_particles	60006

fit	/app/data/saxs_computation/u3/9u3k/9u3k.fit
pddf	/app/data/pr_computation/u3/9u3k/9u3k.pr.out
profile	/app/data/saxs_computation/u3/9u3k/9u3k.dat