← Back to search

9uvo

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

Method: X-RAY DIFFRACTION D_max: 102.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9uvo
deposition_date	2025-05-10
last_revision	2026-05-13
title	Crystal structure of UMPK from S. aureus in complex with UDP
keywords	Allosteric effect, hexamers, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.73 Å
rg_electron	31.30 Å
i0	104908000.00
molecular_weight	79241.0 kDa
excluded_volume	98635 Å³
envelope_volume	126020 Å³
shell_volume	34173 Å³
envelope_diameter	113.2 Å
shell_rg	37.17 Å
envelope_rg	31.64 Å
shape_rg	31.33 Å
total_rg	31.70 Å
total_atoms	5517
n_residues	711
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

▼

3. P(r) Analysis (GNOM)

dmax	102.8 Å
rg_real	31.70 Å
rg_real_error	0.94 Å
i0_real	1.0490e+08
i0_real_error	1.9130e+06
rg_reciprocal	31.72 Å
i0_reciprocal	104900000.0000
total_estimate	0.9007
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.9 Å
skewness	0.219
kurtosis	-0.612
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	16940000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.955

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

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	B,A,C
atom_count	5529

MGHHHHHHMAQISKYKRVVLKLSGEALAGEKGFGINPVIIKSVAEQVAEVAKMDCEIAVIVGGGNIWRGKTGSDLGMDRGTADYMGMLATVMNALALQDSLEQLDCDTRVLTSIEMKQVAEPYIRRRAIRHLEKKRVVIFAAGIGNPYFSTDTTAALRAAEVEADVILMGKNNVDGVYSADPKVNKDAVKYEHLTHIQMLQEGLQVMDSTASSFCMDNNIPLTVFSIMEEGNIKRAVMGEKIGTLITK

Source

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

Entity 2 non-polymer

description	URIDINE-5'-DIPHOSPHATE
formula_weight	404.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	12

▶

6. Citations (1)

▶

length_a	73.345 Å
length_b	73.345 Å
length_c	301.410 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	2.750 Å
resolution_low	49.040 Å
r_factor	0.2129
r_work	0.2106
r_free	0.2562

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