← Back to search

9ufi

Crystal structure of a PhGs rhamnosyltransferase UGT79G15 from Rehmannia glutinosa in complex with UDP and FSA

Method: X-RAY DIFFRACTION D_max: 126.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ufi
deposition_date	2025-04-10
title	Crystal structure of a PhGs rhamnosyltransferase UGT79G15 from Rehmannia glutinosa in complex with UDP and FSA
keywords	catalysis, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.20 Å
rg_electron	36.32 Å
i0	303154000.00
molecular_weight	95184.0 kDa
excluded_volume	92721 Å³
envelope_volume	161490 Å³
shell_volume	39517 Å³
envelope_diameter	134.1 Å
shell_rg	39.32 Å
envelope_rg	36.39 Å
shape_rg	36.31 Å
total_rg	36.48 Å
total_atoms	7200
n_residues	900
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	126.4 Å
rg_real	36.66 Å
rg_real_error	1.41 Å
i0_real	3.0320e+08
i0_real_error	6.0590e+06
rg_reciprocal	36.37 Å
i0_reciprocal	303100000.0000
total_estimate	0.5652
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	31.6 Å
skewness	0.634
kurtosis	-0.194
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	37820000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.609; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.656; Smooth: 0.557

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	UGT79G15
formula_weight	50913.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7325

MPEFEKPKLHITMFPWVAIGHITPFIHLANELAKRGHSISILIPKKAHTQLGHNNLYPDLIKFHIVTVPHVEGLPAGAETASDIDITAKNPLAIAFDAMYEQVETLLYGLKPDIVFYDFADWIPKLAAQIGFKTVCYNVICASCMAIGIVPARHIPKDRPLTEEELMTPPEGYPSSTVVLRGQEARTLSFIGMDYGATKFDVRITAAMQGCDAIGIRTCRELEGPMCDYLSAQYNKPVFLSGPVLPESPKGPLEEKWEKWLNKFEPKSVVYCAFGSQMILQKNQFQELVLGFEMTGLPFFVALSKPHGADSIEEALPEGFLERVGDRGVVHGGWVQQTQILNHQSVGCFVSHCGFGSMWESLLSDSQIVLVPRLADQILNTRLLAEELKVAVEVERGDMGWFSKEDLCKAIKSVMDEESEVGKLVKKNHAKWRETLVSPGYMDNYLEDFIQQLYG

Source

organism	Rehmannia glutinosa
ncbi_taxonomy_id	99300
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	Forsythiaside A
formula_weight	624.6 kDa
src_method	nat
entity_count	2

Entity 3 non-polymer

description	URIDINE-5'-DIPHOSPHATE
formula_weight	404.2 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	125

▶

6. Citations (1)

▶

length_a	46.105 Å
length_b	73.244 Å
length_c	134.294 Å
angle_alpha	90.00 °
angle_beta	97.52 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.120 Å
resolution_low	49.260 Å
r_factor	0.2021
r_work	0.1996
r_free	0.2476

fit	/app/data/saxs_computation/uf/9ufi/9ufi.fit
pddf	/app/data/pr_computation/uf/9ufi/9ufi.pr.out
profile	/app/data/saxs_computation/uf/9ufi/9ufi.dat

Crystal structure of a PhGs rhamnosyltransferase UGT79G15 from Rehmannia glutinosa in complex with UDP and FSA

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