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9v16

Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP

Method: X-RAY DIFFRACTION D_max: 151.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v16
deposition_date	2025-05-19
title	Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant 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	48.62 Å
rg_electron	47.81 Å
i0	1924080000.00
molecular_weight	365240.0 kDa
excluded_volume	456200 Å³
envelope_volume	613950 Å³
shell_volume	101860 Å³
envelope_diameter	156.8 Å
shell_rg	56.95 Å
envelope_rg	46.27 Å
shape_rg	47.80 Å
total_rg	48.15 Å
total_atoms	25769
n_residues	3171
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	151.7 Å
rg_real	48.23 Å
rg_real_error	1.01 Å
i0_real	1.9240e+09
i0_real_error	3.2700e+07
rg_reciprocal	48.62 Å
i0_reciprocal	1925000000.0000
total_estimate	0.8929
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.3 Å
skewness	0.024
kurtosis	-0.600
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	287100000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.897

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Glycogen phosphorylase
formula_weight	93626.6 kDa
ec_number	2.4.1.1
mutation	N185A/R267E
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	25769

MGMNAPFTYSSPTLSVEALKHSIAYKLMFTIGKDPVVANKHEWLNATLFAVRDRLVERWLRSNRAQLSQETRQVYYLSMEFLIGRTLSNAMLSLGIYEDVQGALEAMGLNLEELIDEENDPGLGNGGLGRLAACFLDSLATLGLPGRGYGIRYDYGMFKQNIVNGSQKESPDYWLEYGNPWEFKRHATRYKVRFGGRIQQEGKKTRWIETEEILGVAYDQIIPGYDTDATNTLRLWSAQASSEINLGKFNQGDYFAAVEDKNHSENVSEVLYPDDSTYSGRELRLRQEYFLVSSTIQDILSRHYQLHKTYDNLADKIAIHLNDTHPVLSIPEMMRLLIDEHQFSWDDAFEVCCQVFSYTNHTLMSEALETWPVDMLGKILPRHLQIIFEINDYFLKTLQEQYPNDTDLLGRASIIDESNGRRVRMAWLAVVVSHKVNGVSELHSNLMVQSLFADFAKIFPGRFTNVTNGVTPRRWLAVANPSLSAVLDEHLGRNWRTDLSLLNELQQHCDFPMVNHAVHQAKLENKKRLAEYIAQQLNVVVNPKALFDVQIKRIHEYKRQLMNVLHVITRYNRIKADPDAKWVPRVNIFGGKAASAYYMAKHIIHLINDVAKVINNDPQIGDKLKVVFIPNYSVSLAQLIIPAADLSEQISLAGTEASGTSNMKFALNGALTIGTLDGANVEMLDHVGADNIFIFGNTAEEVEELRRQGYKPREYYEKDEELHQVLTQIGSGVFSPEDPGRYRDLVDSLINFGDHYQVLADYRSYVDCQDKVDELYELQEEWTAKAMLNIANMGYFSSDRTIKEYADHIWHIDPVRL

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
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	185.604 Å
length_b	185.604 Å
length_c	451.242 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	3.450 Å
resolution_low	49.450 Å
r_factor	0.1942
r_work	0.1921
r_free	0.2351

fit	/app/data/saxs_computation/v1/9v16/9v16.fit
pddf	/app/data/pr_computation/v1/9v16/9v16.pr.out
profile	/app/data/saxs_computation/v1/9v16/9v16.dat

Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant 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)