← Back to search

9yfb

Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with UTP

Method: X-RAY DIFFRACTION D_max: 68.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yfb
deposition_date	2025-09-25
last_revision	2025-10-08
title	Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with UTP
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.08 Å
rg_electron	18.90 Å
i0	15642200.00
molecular_weight	29826.0 kDa
excluded_volume	37457 Å³
envelope_volume	44445 Å³
shell_volume	19759 Å³
envelope_diameter	69.2 Å
shell_rg	25.43 Å
envelope_rg	19.34 Å
shape_rg	18.91 Å
total_rg	19.83 Å
total_atoms	2096
n_residues	272
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	68.8 Å
rg_real	20.03 Å
rg_real_error	0.51 Å
i0_real	1.5640e+07
i0_real_error	2.0520e+05
rg_reciprocal	20.04 Å
i0_reciprocal	15640000.0000
total_estimate	0.8522
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.6 Å
skewness	0.348
kurtosis	-0.018
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	3449000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.695; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.993

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

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	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2222

MAHHHHHHVVRKAVFPVAGMGTRFLPATKAMPKEMLPVVDKPLIQYAVEEAVAAGITDLIFVTGRNKRAIEDHFDAAPELETDLEAKGKHELLALVRDILPAHVNCLYIRQSAPLGLGHAVLTAAPAVGNEPFAVLLADDLIDADTPVLKQLIDVAVARQGSVLGVQEVPREDTRKYGIVASQPVDARTERVTHIVEKPAPEQAPTTLAVVGRYVLEAAIFDHLRATTVGAGNEIQLTDGIAALLRERDVYAHRYDGKRYDCGSKAGMFQATVALGRKYHGLIPE

Source

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

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	;URIDINE 5'-TRIPHOSPHATE ;
formula_weight	484.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	110

▶

6. Citations (1)

▶

length_a	73.672 Å
length_b	73.672 Å
length_c	118.422 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 42 21 2
int_tables_number	94
crystal_system	—

resolution	1.820 Å
resolution_low	47.680 Å
r_factor	0.2003
r_work	0.1987
r_free	0.2319

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

Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with UTP

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