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9ygk

Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis (sulfate bound)

Method: X-RAY DIFFRACTION D_max: 89.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ygk
deposition_date	2025-09-29
last_revision	2025-10-08
title	Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis (sulfate bound)
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, 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	27.66 Å
rg_electron	26.39 Å
i0	63718400.00
molecular_weight	60404.0 kDa
excluded_volume	75043 Å³
envelope_volume	95011 Å³
shell_volume	30406 Å³
envelope_diameter	91.8 Å
shell_rg	33.23 Å
envelope_rg	26.67 Å
shape_rg	26.36 Å
total_rg	27.23 Å
total_atoms	4219
n_residues	543
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	89.2 Å
rg_real	27.67 Å
rg_real_error	0.63 Å
i0_real	6.3720e+07
i0_real_error	7.8880e+05
rg_reciprocal	27.67 Å
i0_reciprocal	63720000.0000
total_estimate	0.8912
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.7 Å
skewness	0.371
kurtosis	-0.348
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	9621000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.929

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	UTP--glucose-1-phosphate uridylyltransferase
formula_weight	30991.6 kDa
ec_number	2.7.7.9
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4467

MAHHHHHHVVRKAVFPVAGMGTRFLPATKAMPKEMLPVVDKPLIQYAVEEAVAAGITDLIFVTGRNKRAIEDHFDAAPELETDLEAKGKHELLALVRDILPAHVNCLYIRQSAPLGLGHAVLTAAPAVGNEPFAVLLADDLIDADTPVLKQLIDVAVARQGSVLGVQEVPREDTRKYGIVASQPVDARTERVTHIVEKPAPEQAPTTLAVVGRYVLEAAIFDHLRATTVGAGNEIQLTDGIAALLRERDVYAHRYDGKRYDCGSKAGMFQATVALGRKYHGLIPE

Source

organism	Bordetella pertussis Tohama I
ncbi_taxonomy_id	257313
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	19

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	229

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6. Citations (1)

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length_a	116.246 Å
length_b	95.799 Å
length_c	81.205 Å
angle_alpha	90.00 °
angle_beta	110.36 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.950 Å
resolution_low	47.160 Å
r_factor	0.1862
r_work	0.1843
r_free	0.2232

fit	/app/data/saxs_computation/yg/9ygk/9ygk.fit
pddf	/app/data/pr_computation/yg/9ygk/9ygk.pr.out
profile	/app/data/saxs_computation/yg/9ygk/9ygk.dat