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9uf7

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

Method: X-RAY DIFFRACTION D_max: 124.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uf7
deposition_date	2025-04-10
title	Crystal structure of a PhGs rhamnosyltransferase UGT79G15 from Rehmannia glutinosa in complex with UDP
keywords	catalysis, 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	36.43 Å
rg_electron	36.40 Å
i0	149390000.00
molecular_weight	100920.0 kDa
excluded_volume	127310 Å³
envelope_volume	161800 Å³
shell_volume	39578 Å³
envelope_diameter	132.7 Å
shell_rg	39.33 Å
envelope_rg	36.44 Å
shape_rg	36.40 Å
total_rg	36.59 Å
total_atoms	7097
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

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3. P(r) Analysis (GNOM)

dmax	124.9 Å
rg_real	36.89 Å
rg_real_error	1.12 Å
i0_real	1.4940e+08
i0_real_error	2.4150e+06
rg_reciprocal	36.61 Å
i0_reciprocal	149300000.0000
total_estimate	0.7738
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.9 Å
skewness	0.629
kurtosis	-0.214
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	41410000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.642; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.651; Smooth: 0.479

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	UGT79G15
formula_weight	50279.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7283

KPKLHITMFPWVAIGHITPFIHLANELAKRGHSISILIPKKAHTQLGHNNLYPDLIKFHIVTVPHVEGLPAGAETASDIDITAKNPLAIAFDAMYEQVETLLYGLKPDIVFYDFADWIPKLAAQIGFKTVCYNVICASCMAIGIVPARHIPKDRPLTEEELMTPPEGYPSSTVVLRGQEARTLSFIGMDYGATKFDVRITAAMQGCDAIGIRTCRELEGPMCDYLSAQYNKPVFLSGPVLPESPKGPLEEKWEKWLNKFEPKSVVYCAFGSQMILQKNQFQELVLGFEMTGLPFFVALSKPHGADSIEEALPEGFLERVGDRGVVHGGWVQQTQILNHQSVGCFVSHCGFGSMWESLLSDSQIVLVPRLADQILNTRLLAEELKVAVEVERGDMGWFSKEDLCKAIKSVMDEESEVGKLVKKNHAKWRETLVSPGYMDNYLEDFIQQLYG

Source

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

Entity 2 non-polymer

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

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	186

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6. Citations (1)

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length_a	46.254 Å
length_b	72.059 Å
length_c	134.360 Å
angle_alpha	90.00 °
angle_beta	97.83 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.400 Å
resolution_low	48.890 Å
r_factor	0.2080
r_work	0.2060
r_free	0.2490

fit	/app/data/saxs_computation/uf/9uf7/9uf7.fit
pddf	/app/data/pr_computation/uf/9uf7/9uf7.pr.out
profile	/app/data/saxs_computation/uf/9uf7/9uf7.dat

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

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