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9uy2

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

Method: X-RAY DIFFRACTION D_max: 110.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uy2
deposition_date	2025-05-14
last_revision	2026-05-27
title	Crystal structure of UMPK from S. aureus in complex with ATP
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	33.94 Å
rg_electron	33.28 Å
i0	392701000.00
molecular_weight	157610.0 kDa
excluded_volume	196760 Å³
envelope_volume	244320 Å³
shell_volume	58215 Å³
envelope_diameter	119.9 Å
shell_rg	42.07 Å
envelope_rg	33.56 Å
shape_rg	33.30 Å
total_rg	33.84 Å
total_atoms	10982
n_residues	1421
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	110.3 Å
rg_real	33.77 Å
rg_real_error	0.62 Å
i0_real	3.9270e+08
i0_real_error	5.6580e+06
rg_reciprocal	33.87 Å
i0_reciprocal	392700000.0000
total_estimate	0.8788
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.6 Å
skewness	0.188
kurtosis	-0.329
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	129800000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.957

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	11001

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	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	19

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6. Citations (1)

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length_a	75.781 Å
length_b	114.709 Å
length_c	99.206 Å
angle_alpha	90.00 °
angle_beta	90.58 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.819 Å
resolution_low	30.194 Å
r_factor	0.1935
r_work	0.1914
r_free	0.2325

fit	/app/data/saxs_computation/uy/9uy2/9uy2.fit
pddf	/app/data/pr_computation/uy/9uy2/9uy2.pr.out
profile	/app/data/saxs_computation/uy/9uy2/9uy2.dat

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

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