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9w47

Structure of protein O-glucosyltransferase 2 with UDP

Method: X-RAY DIFFRACTION D_max: 77.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w47
deposition_date	2025-07-31
last_revision	2026-03-11
title	Structure of protein O-glucosyltransferase 2 with UDP
keywords	secretory protein, O-glucosyltransferase, 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	24.56 Å
rg_electron	23.58 Å
i0	48198600.00
molecular_weight	54836.0 kDa
excluded_volume	68997 Å³
envelope_volume	80961 Å³
shell_volume	28200 Å³
envelope_diameter	78.3 Å
shell_rg	31.16 Å
envelope_rg	23.80 Å
shape_rg	23.57 Å
total_rg	24.47 Å
total_atoms	3867
n_residues	468
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	77.7 Å
rg_real	24.44 Å
rg_real_error	0.39 Å
i0_real	4.8200e+07
i0_real_error	5.7150e+05
rg_reciprocal	24.47 Å
i0_reciprocal	48200000.0000
total_estimate	0.9057
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.4 Å
skewness	0.186
kurtosis	-0.557
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	11940000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protein O-glucosyltransferase 2
formula_weight	57536.8 kDa
ec_number	2.4.1.-,2.4.2.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4032

MFGTLLLYCFFLATVPALAETGGERQLSPEKSEIWGPGLKADVVLPARYFYIQAVDTSGNKFTSSPGEKVFQVKVSAPEEQFTRVGVQVLDRKDGSFIVRYRMYASYKNLKVEIKFQGQHVAKSPYILKGPVYHENCDCPLQDSAAWLREMNCPETIAQIQRDLAHFPAVDPEKIAVEIPKRFGQRQSLCHYTLKDNKVYIKTHGEHVGFRIFMDAILLSLTRKVKMPDVELFVNLGDWPLEKKKSNSNIHPIFSWCGSTDSKDIVMPTYDLTDSVLETMGRVSLDMMSVQANTGPPWESKNSTAVWRGRDSRKERLELVKLSRKHPELIDAAFTNFFFFKHDENLYGPIVKHISFFDFFKHKYQINIDGTVAAYRLPYLLVGDSVVLKQDSIYYEHFYNELQPWKHYIPVKSNLSDLLEKLKWAKDHDEEAKKIAKAGQEFARNNLMGDDIFCYYFKLFQEYANLQVSEPQIREGMKRVEPQTEDDLFPCTCHRKK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Komagataella pastoris

Entity 2 non-polymer

description	URIDINE-5'-DIPHOSPHATE
formula_weight	404.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	165

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6. Citations (1)

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length_a	47.130 Å
length_b	63.280 Å
length_c	89.530 Å
angle_alpha	90.00 °
angle_beta	95.96 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.790 Å
resolution_low	29.680 Å
r_factor	0.2077
r_work	0.2064
r_free	0.2328

fit	/app/data/saxs_computation/w4/9w47/9w47.fit
pddf	/app/data/pr_computation/w4/9w47/9w47.pr.out
profile	/app/data/saxs_computation/w4/9w47/9w47.dat

Structure of protein O-glucosyltransferase 2 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