Oligomer structure of a glycosyltransferase

Method: ELECTRON MICROSCOPY D_max: 164.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u7j
deposition_date	2025-03-24
title	Oligomer 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	53.75 Å
rg_electron	53.53 Å
i0	1922980000.00
molecular_weight	366340.0 kDa
excluded_volume	458560 Å³
envelope_volume	704780 Å³
shell_volume	109230 Å³
envelope_diameter	173.0 Å
shell_rg	56.45 Å
envelope_rg	52.97 Å
shape_rg	53.53 Å
total_rg	53.64 Å
total_atoms	25776
n_residues	3120
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	164.5 Å
rg_real	53.58 Å
rg_real_error	1.11 Å
i0_real	1.9230e+09
i0_real_error	3.7950e+07
rg_reciprocal	53.88 Å
i0_reciprocal	1924000000.0000
total_estimate	0.6255
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	68.1 Å
skewness	0.196
kurtosis	-0.428
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	92990000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.971; Smooth: 0.265

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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	60566.6 kDa
ec_number	2.4.1.50
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	a,A,B,C,D,E
atom_count	25776

ERWSPESPLQAPRVLIALLARNAAHALPTTLGALERLRHPRERTALWVATDHNMDNTSTVLREWLVAVKSLYHSVEWRPAEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILFVDADNLILNPDTLSLLIAENKTVVAPMLDSRAAYSNFWCGMTSQGYYKRTPAYIPIRKRDRRGCFAVPMVHSTFLIDLRKAASRNLAFYPPHPDYTWSFDDIIVFAFSCKQAEVQMYVCNKEEYGFLPVPLRAHSTLQDEAESFMHVQLEVMVKHPPAEPSRFISAPTKTPDKMGFDEVFMINLRRRQDRRERMLRALQAQEIECRLVEAVDGKAMNTSQVEALGIQMLPGYRDPYHGRPLTKGELGCFLSHYNIWKEVVDRGLQKSLVFEDDLRFEIFFKRRLMNLMRDVEREGLDWDLIYVGRKRMQVEHPEKAVPRVRNLVEADYSYWTLAYVISLQGARKLLAAEPLSKMLPVDEFLPVMFDKHPVSEYKAHFSLRNLHAFSVEPLLIYPTH

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	6

Entity 3 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	6

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6. Citations (1)

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resolution	3.30 Å
resolution_method	—
num_particles	375486

fit	/app/data/saxs_computation/u7/9u7j/9u7j.fit
pddf	/app/data/pr_computation/u7/9u7j/9u7j.pr.out
profile	/app/data/saxs_computation/u7/9u7j/9u7j.dat