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9uvn

Crystal structure of UMPK from S. aureus in complex with U5P

Method: X-RAY DIFFRACTION D_max: 104.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uvn
deposition_date	2025-05-10
last_revision	2026-05-13
title	Crystal structure of UMPK from S. aureus in complex with U5P
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	32.06 Å
rg_electron	31.46 Å
i0	96745800.00
molecular_weight	77373.0 kDa
excluded_volume	96891 Å³
envelope_volume	124820 Å³
shell_volume	33880 Å³
envelope_diameter	112.0 Å
shell_rg	37.32 Å
envelope_rg	31.63 Å
shape_rg	31.47 Å
total_rg	31.94 Å
total_atoms	5400
n_residues	708
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	104.2 Å
rg_real	32.02 Å
rg_real_error	0.68 Å
i0_real	9.6750e+07
i0_real_error	1.4320e+06
rg_reciprocal	32.04 Å
i0_reciprocal	96750000.0000
total_estimate	0.8988
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	31.9 Å
skewness	0.205
kurtosis	-0.624
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	19680000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.964

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Uridylate kinase
formula_weight	27193.5 kDa
ec_number	2.7.4.22
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,A,B
atom_count	5408

MGHHHHHHMAQISKYKRVVLKLSGEALAGEKGFGINPVIIKSVAEQVAEVAKMDCEIAVIVGGGNIWRGKTGSDLGMDRGTADYMGMLATVMNALALQDSLEQLDCDTRVLTSIEMKQVAEPYIRRRAIRHLEKKRVVIFAAGIGNPYFSTDTTAALRAAEVEADVILMGKNNVDGVYSADPKVNKDAVKYEHLTHIQMLQEGLQVMDSTASSFCMDNNIPLTVFSIMEEGNIKRAVMGEKIGTLITK

Source

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

Entity 2 non-polymer

description	URIDINE-5'-MONOPHOSPHATE
formula_weight	324.2 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	8

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6. Citations (1)

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length_a	117.357 Å
length_b	96.302 Å
length_c	75.840 Å
angle_alpha	90.00 °
angle_beta	103.45 °
angle_gamma	90.00 °
z_pdb	12

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.260 Å
resolution_low	13.033 Å
r_factor	0.2380
r_work	0.2360
r_free	0.2763

fit	/app/data/saxs_computation/uv/9uvn/9uvn.fit
pddf	/app/data/pr_computation/uv/9uvn/9uvn.pr.out
profile	/app/data/saxs_computation/uv/9uvn/9uvn.dat

Crystal structure of UMPK from S. aureus in complex with U5P

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