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9yfk

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

Method: X-RAY DIFFRACTION D_max: 88.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yfk
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 (twinned lattice) ;
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	26.88 Å
rg_electron	26.01 Å
i0	60985600.00
molecular_weight	61201.0 kDa
excluded_volume	76838 Å³
envelope_volume	90536 Å³
shell_volume	29813 Å³
envelope_diameter	91.1 Å
shell_rg	32.79 Å
envelope_rg	26.00 Å
shape_rg	26.04 Å
total_rg	26.63 Å
total_atoms	4304
n_residues	556
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	88.8 Å
rg_real	26.99 Å
rg_real_error	0.62 Å
i0_real	6.0990e+07
i0_real_error	9.2890e+05
rg_reciprocal	26.96 Å
i0_reciprocal	60980000.0000
total_estimate	0.8660
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.494
kurtosis	-0.237
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	19300000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.894

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4. Crystallography & Experiment

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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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4629

MAHHHHHHVVRKAVFPVAGMGTRFLPATKAMPKEMLPVVDKPLIQYAVEEAVAAGITDLIFVTGRNKRAIEDHFDAAPELETDLEAKGKHELLALVRDILPAHVNCLYIRQSAPLGLGHAVLTAAPAVGNEPFAVLLADDLIDADTPVLKQLIDVAVARQGSVLGVQEVPREDTRKYGIVASQPVDARTERVTHIVEKPAPEQAPTTLAVVGRYVLEAAIFDHLRATTVGAGNEIQLTDGIAALLRERDVYAHRYDGKRYDCGSKAGMFQATVALGRKYHGLIPE

Source

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

Entity 2 non-polymer

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

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	283

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6. Citations (1)

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length_a	93.397 Å
length_b	71.027 Å
length_c	93.487 Å
angle_alpha	90.00 °
angle_beta	90.06 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.680 Å
resolution_low	46.740 Å
r_factor	0.1777
r_work	0.1679
r_free	0.2045

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

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

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