SAXSdb — 9yq4

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1. Structure Basics

entry_id	9yq4
deposition_date	2025-10-15
last_revision	2025-12-10
title	Chlorella virus hyaluronan synthase bound to a proofreading UDP-GlcA
keywords	Glycosyltransferase, Membrane Protein, Hyaluronan Synthase, Substrate, TRANSFERASE-IMMUNE SYSTEM complex; TRANSFERASE/IMMUNE SYSTEM
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	36.79 Å
rg_electron	36.92 Å
i0	107133000.00
molecular_weight	85070.0 kDa
excluded_volume	107260 Å³
envelope_volume	138330 Å³
shell_volume	36090 Å³
envelope_diameter	145.6 Å
shell_rg	36.93 Å
envelope_rg	37.44 Å
shape_rg	36.92 Å
total_rg	36.92 Å
total_atoms	5993
n_residues	739
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	136.0 Å
rg_real	37.58 Å
rg_real_error	1.62 Å
i0_real	1.0710e+08
i0_real_error	2.0610e+06
rg_reciprocal	37.09 Å
i0_reciprocal	107100000.0000
total_estimate	0.7080
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	31.6 Å
skewness	0.767
kurtosis	0.012
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	14350000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.412; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.223; Smooth: 0.740

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Hyaluronan synthase
formula_weight	65889.1 kDa
ec_number	2.4.1.212
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5993

MGTSWRTIVSANLFAVGGALLMLAPAIVGYVFQWNIGVSAVWGISVYGVFVLGFYIAQIVFSEFNRMRLSDWISLRPDNWNATRVAVIIAGYREDPFMFKKCLESVRDSEYGNVARLICVIDGDEEEDLKMAEIYKQVYNDNVKKPGVVLCESENKNGSTIDSDVSKNICILQPHRGKRESLYTGFQLASMDPSVHAVVLIDSDTVLEKNAILEVVYPLSCDPNIKAVAGECKIWNTDTILSMLVSWRYFSAFNVERGAQSLWKTVQCVGGPLGAYTIDIINEIKDPWITQTFLGNKCTYGDNRRLTNEVLMRGKKIVYTPFAVGWSDSPTNVMRYIVQQTRWSKSWCREIWYTLGSAWKHGFSGIYLAFECMYQIMYFFLVMYLFSYIAIKADIRAQTATVLVSTLVTIIKSSYLALRAKNLKAFYFVLYTYVYFFCMIPARITAMFTMFDIAWGTRGGNAKMTIGARVWLWAKQFLITYMWWAGVLAAGVYSIVDNWYFDWADIQYRFALVGICSYLVFVSIVLVIYLIGKITTWNYTPLQKELIEERYLHNASENAPEVLEHHHHHHHHHH

Source

organism	Paramecium bursaria Chlorella virus CZ-2
ncbi_taxonomy_id	1278251
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	nanobody Nb872
formula_weight	14783.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVQLVESGGGLVQAGGSLKVSCAASGRAFKTYRMAWFRQAPGKEREFVSGISALETTYYADSVKGRFTISRDNTKNTVSLQMDSLKPEDTAVYYCAARRYGGTDYTTTGSYDYWGQGTQVTVSSHHHHHHEPEA

Source

organism	Lama glama
common_name	llama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	nanobody Nb881
formula_weight	14956.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QVQLVESGGGLVQAGGSLRLACAASGRIFSSDTLAWFRRAPGKEREFVAASRWSGGGTDYADSVKGRFTFSRDNTFNTMCLEMNSLKPEDTAVYYCALRTARDSYYYTRNPTGYDYWGQGTQSSHHHHHHEPEA

Source

organism	Lama glama
common_name	llama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	;URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID ;
formula_weight	580.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	CHOLESTEROL HEMISUCCINATE
formula_weight	486.7 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	3.30 Å
resolution_method	—
num_particles	64146

fit	/app/data/saxs_computation/yq/9yq4/9yq4.fit
pddf	/app/data/pr_computation/yq/9yq4/9yq4.pr.out
profile	/app/data/saxs_computation/yq/9yq4/9yq4.dat

Chlorella virus hyaluronan synthase bound to a proofreading UDP-GlcA

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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)