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9uvp

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

Method: X-RAY DIFFRACTION D_max: 103.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uvp
deposition_date	2025-05-10
last_revision	2026-05-13
title	Crystal structure of UMPK from S. aureus in complex with ATP and 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	31.46 Å
rg_electron	31.09 Å
i0	105420000.00
molecular_weight	79381.0 kDa
excluded_volume	98777 Å³
envelope_volume	125560 Å³
shell_volume	34134 Å³
envelope_diameter	110.9 Å
shell_rg	37.10 Å
envelope_rg	31.53 Å
shape_rg	31.12 Å
total_rg	31.49 Å
total_atoms	5528
n_residues	712
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	103.0 Å
rg_real	31.44 Å
rg_real_error	0.77 Å
i0_real	1.0540e+08
i0_real_error	1.7000e+06
rg_reciprocal	31.45 Å
i0_reciprocal	105400000.0000
total_estimate	0.8999
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.9 Å
skewness	0.230
kurtosis	-0.600
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	15830000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.976

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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	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	5540

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	2

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	12

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6. Citations (1)

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length_a	72.551 Å
length_b	72.551 Å
length_c	298.059 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	2.568 Å
resolution_low	48.508 Å
r_factor	0.2153
r_work	0.2137
r_free	0.2450

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