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9yfi

;Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE ;

Method: X-RAY DIFFRACTION D_max: 87.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yfi
deposition_date	2025-09-26
last_revision	2025-10-08
title	;Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with URIDINE-5'-DIPHOSPHATE-GLUCOSE ;
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	26.70 Å
rg_electron	25.90 Å
i0	57984300.00
molecular_weight	59696.0 kDa
excluded_volume	74975 Å³
envelope_volume	88138 Å³
shell_volume	29250 Å³
envelope_diameter	89.9 Å
shell_rg	32.59 Å
envelope_rg	25.96 Å
shape_rg	25.94 Å
total_rg	26.47 Å
total_atoms	4195
n_residues	540
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	87.4 Å
rg_real	26.82 Å
rg_real_error	0.67 Å
i0_real	5.7980e+07
i0_real_error	8.7630e+05
rg_reciprocal	26.79 Å
i0_reciprocal	57980000.0000
total_estimate	0.8641
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.1 Å
skewness	0.519
kurtosis	-0.181
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	15130000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.831

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	4472

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	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	URIDINE-5'-DIPHOSPHATE-GLUCOSE
formula_weight	566.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	260

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6. Citations (1)

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length_a	93.234 Å
length_b	71.301 Å
length_c	95.027 Å
angle_alpha	90.00 °
angle_beta	90.86 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.800 Å
resolution_low	47.510 Å
r_factor	0.1728
r_work	0.1714
r_free	0.1994

fit	/app/data/saxs_computation/yf/9yfi/9yfi.fit
pddf	/app/data/pr_computation/yf/9yfi/9yfi.pr.out
profile	/app/data/saxs_computation/yf/9yfi/9yfi.dat