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9ukr

Crystal structure of glycogen phosphorylase from E. coli in complex with AMP

Method: X-RAY DIFFRACTION D_max: 205.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ukr
deposition_date	2025-04-18
title	Crystal structure of glycogen phosphorylase from E. coli in complex with AMP
keywords	glycogen phosphorylase, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

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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	65.24 Å
rg_electron	65.80 Å
i0	4378770000.00
molecular_weight	555420.0 kDa
excluded_volume	693250 Å³
envelope_volume	975410 Å³
shell_volume	126870 Å³
envelope_diameter	232.0 Å
shell_rg	62.82 Å
envelope_rg	64.98 Å
shape_rg	65.80 Å
total_rg	65.76 Å
total_atoms	39190
n_residues	4818
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	205.4 Å
rg_real	65.77 Å
rg_real_error	1.57 Å
i0_real	4.3780e+09
i0_real_error	9.1980e+07
rg_reciprocal	64.70 Å
i0_reciprocal	4370000000.0000
total_estimate	0.5973
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	68.5 Å
skewness	0.507
kurtosis	-0.355
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0005
highest_alpha	218300000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 0.999; Sysdev: 0.013; Positv: 1.000; Valcen: 0.997; Smooth: 0.037

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Glycogen phosphorylase
formula_weight	93697.7 kDa
ec_number	2.4.1.1
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	39190

MGMNAPFTYSSPTLSVEALKHSIAYKLMFTIGKDPVVANKHEWLNATLFAVRDRLVERWLRSNRAQLSQETRQVYYLSMEFLIGRTLSNAMLSLGIYEDVQGALEAMGLNLEELIDEENDPGLGNGGLGRLAACFLDSLATLGLPGRGYGIRYDYGMFKQNIVNGSQKESPDYWLEYGNPWEFKRHNTRYKVRFGGRIQQEGKKTRWIETEEILGVAYDQIIPGYDTDATNTLRLWSAQASSEINLGKFNQGDYFAAVEDKNHSENVSRVLYPDDSTYSGRELRLRQEYFLVSSTIQDILSRHYQLHKTYDNLADKIAIHLNDTHPVLSIPEMMRLLIDEHQFSWDDAFEVCCQVFSYTNHTLMSEALETWPVDMLGKILPRHLQIIFEINDYFLKTLQEQYPNDTDLLGRASIIDESNGRRVRMAWLAVVVSHKVNGVSELHSNLMVQSLFADFAKIFPGRFTNVTNGVTPRRWLAVANPSLSAVLDEHLGRNWRTDLSLLNELQQHCDFPMVNHAVHQAKLENKKRLAEYIAQQLNVVVNPKALFDVQIKRIHEYKRQLMNVLHVITRYNRIKADPDAKWVPRVNIFGGKAASAYYMAKHIIHLINDVAKVINNDPQIGDKLKVVFIPNYSVSLAQLIIPAADLSEQISLAGTEASGTSNMKFALNGALTIGTLDGANVEMLDHVGADNIFIFGNTAEEVEELRRQGYKPREYYEKDEELHQVLTQIGSGVFSPEDPGRYRDLVDSLINFGDHYQVLADYRSYVDCQDKVDELYELQEEWTAKAMLNIANMGYFSSDRTIKEYADHIWHIDPVRL

Source

organism	Escherichia coli K12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 2 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	8

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6. Citations (1)

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length_a	134.915 Å
length_b	204.539 Å
length_c	263.337 Å
angle_alpha	90.00 °
angle_beta	104.57 °
angle_gamma	90.00 °
z_pdb	24

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	3.550 Å
resolution_low	42.790 Å
r_factor	0.2260
r_work	0.2235
r_free	0.2722

fit	/app/data/saxs_computation/uk/9ukr/9ukr.fit
pddf	/app/data/pr_computation/uk/9ukr/9ukr.pr.out
profile	/app/data/saxs_computation/uk/9ukr/9ukr.dat

Crystal structure of glycogen phosphorylase from E. coli in complex with AMP

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

Refinement

Diffraction

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)