Glycogen phosphorylase from Segatella copri decamer in complex with AMP

Method: ELECTRON MICROSCOPY D_max: 177.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9utg
deposition_date	2025-05-03
title	Glycogen phosphorylase from Segatella copri decamer in complex with AMP
keywords	glycogen metabolism, cryo-EM, gut bacteria, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	65.26 Å
rg_electron	64.64 Å
i0	3395280000.00
molecular_weight	495870.0 kDa
excluded_volume	620210 Å³
envelope_volume	963230 Å³
shell_volume	120170 Å³
envelope_diameter	190.6 Å
shell_rg	73.32 Å
envelope_rg	60.55 Å
shape_rg	64.60 Å
total_rg	64.91 Å
total_atoms	34954
n_residues	4255
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	177.9 Å
rg_real	64.86 Å
rg_real_error	1.16 Å
i0_real	3.3950e+09
i0_real_error	7.0800e+07
rg_reciprocal	65.54 Å
i0_reciprocal	3399000000.0000
total_estimate	0.8459
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	103.8 Å
skewness	-0.040
kurtosis	-0.837
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	107000000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.998; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Alpha-glucan family phosphorylase
formula_weight	98795.9 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	34954

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	8

▶

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	—

resolution	3.58 Å
resolution_method	—
num_particles	30003

fit	/app/data/saxs_computation/ut/9utg/9utg.fit
pddf	/app/data/pr_computation/ut/9utg/9utg.pr.out
profile	/app/data/saxs_computation/ut/9utg/9utg.dat