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9u7h

Complex structure of a glycosyltransferase

Method: ELECTRON MICROSCOPY D_max: 90.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u7h
deposition_date	2025-03-24
title	Complex 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	28.80 Å
rg_electron	28.17 Å
i0	67232200.00
molecular_weight	63391.0 kDa
excluded_volume	79036 Å³
envelope_volume	102240 Å³
shell_volume	30764 Å³
envelope_diameter	94.5 Å
shell_rg	34.83 Å
envelope_rg	28.05 Å
shape_rg	28.20 Å
total_rg	28.79 Å
total_atoms	4454
n_residues	537
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	90.0 Å
rg_real	28.86 Å
rg_real_error	0.60 Å
i0_real	6.7230e+07
i0_real_error	1.0210e+06
rg_reciprocal	28.84 Å
i0_reciprocal	67230000.0000
total_estimate	0.6873
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	29.4 Å
skewness	0.390
kurtosis	-0.515
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	17760000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 0.964; Smooth: 0.779

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4454

APPGADAYFPEERWSPESPLQAPRVLIALLARNAAHALPTTLGALERLRHPRERTALWVATDHNMDNTSTVLREWLVAVKSLYHSVEWRPAEEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILFVDADNLILNPDTLSLLIAENKTVVAPMLDSRAAYSNFWCGMTSQGYYKRTPAYIPIRKRDRRGCFAVPMVHSTFLIDLRKAASRNLAFYPPHPDYTWSFDDIIVFAFSCKQAEVQMYVCNKEEYGFLPVPLRAHSTLQDEAESFMHVQLEVMVKHPPAEPSRFISAPTKTPDKMGFDEVFMINLRRRQDRRERMLRALQAQEIECRLVEAVDGKAMNTSQVEALGIQMLPGYRDPYHGRPLTKGELGCFLSHYNIWKEVVDRGLQKSLVFEDDLRFEIFFKRRLMNLMRDVEREGLDWDLIYVGRKRMQVEHPEKAVPRVRNLVEADYSYWTLAYVISLQGARKLLAAEPLSKMLPVDEFLPVMFDKHPVSEYKAHFSLRNLHAFSVEPLLIYPTHYTGDDGYVSDTETSVVWNNEHVKTDWDRAKSQKMREQQALSREAKNSDVLQSPLDSAARGTLEVLFQGPLGSHHHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Komagataella pastoris

Entity 2 polymer

description	SER-GLY-ALA-LYZ-GLY-GLU-LYS-GLY-SER
formula_weight	836.9 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

SGAKGEKGS

Entity 3 non-polymer

description	GALACTOSE-URIDINE-5'-DIPHOSPHATE
formula_weight	566.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

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

Entity 5 non-polymer

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

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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	3.080 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.08 Å
resolution_method	—
num_particles	3033718

fit	/app/data/saxs_computation/u7/9u7h/9u7h.fit
pddf	/app/data/pr_computation/u7/9u7h/9u7h.pr.out
profile	/app/data/saxs_computation/u7/9u7h/9u7h.dat

Complex 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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)