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9uvk

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

Method: X-RAY DIFFRACTION D_max: 199.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uvk
deposition_date	2025-05-10
last_revision	2026-05-13
title	Crystal structure of UMPK from S. aureus in complex with GTP
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	59.96 Å
rg_electron	59.92 Å
i0	3356210000.00
molecular_weight	476810.0 kDa
excluded_volume	593480 Å³
envelope_volume	838380 Å³
shell_volume	115150 Å³
envelope_diameter	207.7 Å
shell_rg	62.11 Å
envelope_rg	58.75 Å
shape_rg	59.93 Å
total_rg	59.93 Å
total_atoms	33197
n_residues	4273
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	199.2 Å
rg_real	59.85 Å
rg_real_error	2.42 Å
i0_real	3.3560e+09
i0_real_error	7.6310e+07
rg_reciprocal	60.00 Å
i0_reciprocal	3357000000.0000
total_estimate	0.8818
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	53.6 Å
skewness	0.150
kurtosis	-0.759
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	785400000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.874

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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	18

Polymer

type	polypeptide(L)
strand_id	C,A,B,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
atom_count	33341

MGHHHHHHMAQISKYKRVVLKLSGEALAGEKGFGINPVIIKSVAEQVAEVAKMDCEIAVIVGGGNIWRGKTGSDLGMDRGTADYMGMLATVMNALALQDSLEQLDCDTRVLTSIEMKQVAEPYIRRRAIRHLEKKRVVIFAAGIGNPYFSTDTTAALRAAEVEADVILMGKNNVDGVYSADPKVNKDAVKYEHLTHIQMLQEGLQVMDSTASSFCMDNNIPLTVFSIMEEGNIKRAVMGEKIGTLITK

Source

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

Entity 2 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	syn
entity_count	18

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	26

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	144

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6. Citations (1)

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length_a	194.263 Å
length_b	194.263 Å
length_c	116.778 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	54

space_group	P 32
int_tables_number	145
crystal_system	trigonal

resolution	2.880 Å
resolution_low	13.142 Å
r_factor	0.2058
r_work	0.2031
r_free	0.2570

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

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

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