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9u7i

Dimer structure of a glycosyltransferase

Method: ELECTRON MICROSCOPY D_max: 161.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u7i
deposition_date	2025-03-24
title	Dimer structure of a glycosyltransferase
keywords	glycosyltransferase, TRANSFERASE; TRANSFERASE
method	ELECTRON MICROSCOPY

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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	47.22 Å
rg_electron	48.64 Å
i0	224363000.00
molecular_weight	122400.0 kDa
excluded_volume	153190 Å³
envelope_volume	223900 Å³
shell_volume	43192 Å³
envelope_diameter	172.1 Å
shell_rg	43.80 Å
envelope_rg	49.12 Å
shape_rg	48.63 Å
total_rg	48.42 Å
total_atoms	8612
n_residues	1042
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	161.9 Å
rg_real	48.28 Å
rg_real_error	2.02 Å
i0_real	2.2440e+08
i0_real_error	4.4380e+06
rg_reciprocal	47.23 Å
i0_reciprocal	224100000.0000
total_estimate	0.6914
solution_quality	REASONABLE a REASONABLE solution
n_peaks	0
r_peak_primary	— Å
skewness	0.673
kurtosis	-0.265
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	18960000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.496; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.465; Smooth: 0.033

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Procollagen galactosyltransferase 1
formula_weight	71070.0 kDa
ec_number	2.4.1.50
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	a,A
atom_count	8612

APPGADAYFPEERWSPESPLQAPRVLIALLARNAAHALPTTLGALERLRHPRERTALWVATDHNMDNTSTVLREWLVAVKSLYHSVEWRPAEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILFVDADNLILNPDTLSLLIAENKTVVAPMLDSRAAYSNFWCGMTSQGYYKRTPAYIPIRKRDRRGCFAVPMVHSTFLIDLRKAASRNLAFYPPHPDYTWSFDDIIVFAFSCKQAEVQMYVCNKEEYGFLPVPLRAHSTLQDEAESFMHVQLEVMVKHPPAEPSRFISAPTKTPDKMGFDEVFMINLRRRQDRRERMLRALQAQEIECRLVEAVDGKAMNTSQVEALGIQMLPGYRDPYHGRPLTKGELGCFLSHYNIWKEVVDRGLQKSLVFEDDLRFEIFFKRRLMNLMRDVEREGLDWDLIYVGRKRMQVEHPEKAVPRVRNLVEADYSYWTLAYVISLQGARKLLAAEPLSKMLPVDEFLPVMFDKHPVSEYKAHFSLRNLHAFSVEPLLIYPTHYTGDDGYVSDTETSVVWNNEHVKTDWDRAKSQKMREQQALSREAKNSDVLQSPLDSAARGTLEVLFQGPLGSHHHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Komagataella pastoris

Entity 2 non-polymer

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

Entity 3 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	375486

fit	/app/data/saxs_computation/u7/9u7i/9u7i.fit
pddf	/app/data/pr_computation/u7/9u7i/9u7i.pr.out
profile	/app/data/saxs_computation/u7/9u7i/9u7i.dat

Dimer structure of a glycosyltransferase

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

EM 3D