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9uyx

Crystal structure of UMPK from S. aureus in complex with UTP

Method: X-RAY DIFFRACTION D_max: 110.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uyx
deposition_date	2025-05-15
last_revision	2026-05-27
title	Crystal structure of UMPK from S. aureus in complex with UTP
keywords	Allosteric effect, hexamers, 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	34.11 Å
rg_electron	33.34 Å
i0	395055000.00
molecular_weight	157760.0 kDa
excluded_volume	196840 Å³
envelope_volume	247080 Å³
shell_volume	58662 Å³
envelope_diameter	119.0 Å
shell_rg	42.13 Å
envelope_rg	33.58 Å
shape_rg	33.35 Å
total_rg	33.91 Å
total_atoms	10989
n_residues	1420
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	110.0 Å
rg_real	33.93 Å
rg_real_error	0.60 Å
i0_real	3.9510e+08
i0_real_error	5.9100e+06
rg_reciprocal	34.04 Å
i0_reciprocal	395100000.0000
total_estimate	0.8839
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.5 Å
skewness	0.167
kurtosis	-0.374
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	159600000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Uridylate kinase
formula_weight	27193.5 kDa
ec_number	2.7.4.22
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	11037

MGHHHHHHMAQISKYKRVVLKLSGEALAGEKGFGINPVIIKSVAEQVAEVAKMDCEIAVIVGGGNIWRGKTGSDLGMDRGTADYMGMLATVMNALALQDSLEQLDCDTRVLTSIEMKQVAEPYIRRRAIRHLEKKRVVIFAAGIGNPYFSTDTTAALRAAEVEADVILMGKNNVDGVYSADPKVNKDAVKYEHLTHIQMLQEGLQVMDSTASSFCMDNNIPLTVFSIMEEGNIKRAVMGEKIGTLITK

Source

organism	Staphylococcus aureus subsp. aureus NCTC 8325
ncbi_taxonomy_id	93061
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	10

Entity 3 non-polymer

description	;URIDINE 5'-TRIPHOSPHATE ;
formula_weight	484.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	URIDINE-5'-DIPHOSPHATE
formula_weight	404.2 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	48

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6. Citations (1)

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length_a	76.940 Å
length_b	114.786 Å
length_c	101.344 Å
angle_alpha	90.00 °
angle_beta	90.63 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.299 Å
resolution_low	46.354 Å
r_factor	0.2018
r_work	0.1998
r_free	0.2420

fit	/app/data/saxs_computation/uy/9uyx/9uyx.fit
pddf	/app/data/pr_computation/uy/9uyx/9uyx.pr.out
profile	/app/data/saxs_computation/uy/9uyx/9uyx.dat