SAXSdb — 9swy

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1. Structure Basics

entry_id	9swy
deposition_date	2025-10-07
title	The structure of AfUAP1 in complex with GlcNAc-1P
keywords	UAP, GlcNAc-1P, conformation, 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	32.36 Å
rg_electron	31.78 Å
i0	166793000.00
molecular_weight	104380.0 kDa
excluded_volume	131270 Å³
envelope_volume	168860 Å³
shell_volume	44282 Å³
envelope_diameter	117.6 Å
shell_rg	38.74 Å
envelope_rg	31.60 Å
shape_rg	31.79 Å
total_rg	32.32 Å
total_atoms	7364
n_residues	951
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	108.4 Å
rg_real	32.38 Å
rg_real_error	0.76 Å
i0_real	1.6680e+08
i0_real_error	2.7600e+06
rg_reciprocal	32.38 Å
i0_reciprocal	166800000.0000
total_estimate	0.8723
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.6 Å
skewness	0.404
kurtosis	-0.214
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	43510000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.844

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	UDP-N-acetylglucosamine diphosphorylase
formula_weight	53880.2 kDa
ec_number	2.7.7.23
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	7589

GPSAEEFQQLRKKYTDAGQGHVFAFVDELQTGERSQLFHQLSSFDPVRINELADKALNPPKADDGPASLEPLPDIATASILDSDPKDLEQWYEEGLKLVAGNKVAVVLMAGGQGTRLGSSAPKGCFDIGLPSHKSLFQIQAERIAKLQLLAQRISGKEAVIPWYVMTSGPTRKPTEEFFEQHKYFGLNKSDVIIFEQGVLPCISNEGKILMESKFKVAVAPDGNGGIYQALLTSGVREDMRKRGIEHIHTYCVDNCLVKVADPVFIGFAASKQVDIATKVVRKRNATESVGLILQKNGKPDVVEYSEIDKETAEAKDPKQPDVLKFRAANIVNHYYSFKFFESIELWAHKLPHHVARKKIPCIKEGTGEFFKPEKPNGIKLEQFVFDVFPMTPLEKFACIEVRREDEFSPLKNARGTGEDDPDTSKRDIMSQGQRWIEKAGGIVITEGDVVGVEVSPLISYGGEGLEFLKGREIKAPAFIEKEE

Source

organism	Aspergillus fumigatus
ncbi_taxonomy_id	746128
host_organism	Escherichia coli

Entity 2 polymer

description	UDP-N-acetylglucosamine diphosphorylase
formula_weight	53823.2 kDa
ec_number	2.7.7.23
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

GPSAEEFQQLRKKYTDAGQGHVFAFVDELQTGERSQLFHQLSSFDPVRINELADKALNPPKADDGPASLEPLPDIATASILDSDPKDLEQWYEEGLKLVAGNKVAVVLMAGGQGTRLGSSAPKGCFDIGLPSHKSLFQIQAERIAKLQLLAQRISGKEAVIPWYVMTSGPTRKPTEEFFEQHKYFGLNKSDVIIFEQGVLPCISNEGKILMESKFKVAVAPDGNGGIYQALLTSGVREDMRKRGIEHIHTYCVDNCLVKVADPVFIGFAASKQVDIATKVVRKRNATESVGLILQKNGKPDVVEYSEIDKETAEAKDPKQPDVLKFRAANIVNHYYSFKFFESIELWAHKLPHHVARKKIPCIKEGTGEFFKPEKPNGIKLEQFVFDVFPMTPLEKFACIEVRREDEFSPLKNARGTGEDDPDTSKRDIMSQGQRWIEKAGGIVITEGDVVGVEVSPLISYGGEGLEFLKGREIKAPAFIEKEE

Source

organism	Aspergillus fumigatus
ncbi_taxonomy_id	746128
host_organism	Escherichia coli

Entity 3 non-polymer

description	2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
formula_weight	301.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	216

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6. Citations (1)

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length_a	55.834 Å
length_b	136.865 Å
length_c	143.081 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.720 Å
resolution_low	71.540 Å
r_factor	0.2111
r_work	0.2104
r_free	0.2519

fit	/app/data/saxs_computation/sw/9swy/9swy.fit
pddf	/app/data/pr_computation/sw/9swy/9swy.pr.out
profile	/app/data/saxs_computation/sw/9swy/9swy.dat

The structure of AfUAP1 in complex with GlcNAc-1P

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)