SAXSdb — 9s6t

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1. Structure Basics

entry_id	9s6t
deposition_date	2025-08-01
title	Ternary cryo-EM structure of chicken ALG12 with Dol25-PP-GlcNAc2Man7, Dol25-P-Man, and Fab
keywords	Mannosyltransferase, ternary complex, N-linked glycosylation, 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	34.21 Å
rg_electron	33.85 Å
i0	190684000.00
molecular_weight	77630.0 kDa
excluded_volume	77037 Å³
envelope_volume	132720 Å³
shell_volume	35120 Å³
envelope_diameter	126.4 Å
shell_rg	37.65 Å
envelope_rg	34.07 Å
shape_rg	33.79 Å
total_rg	34.19 Å
total_atoms	5922
n_residues	708
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	116.5 Å
rg_real	34.51 Å
rg_real_error	1.04 Å
i0_real	1.9070e+08
i0_real_error	3.0550e+06
rg_reciprocal	34.33 Å
i0_reciprocal	190700000.0000
total_estimate	0.8252
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.4 Å
skewness	0.540
kurtosis	-0.355
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	18520000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.795; Smooth: 0.693

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Mannosyltransferase
formula_weight	56295.2 kDa
ec_number	2.4.1.-
mutation	E35Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6007

GPGGSTMAQKRSSSGRSFPLLLLIIVVAFVHLTVCPFTKVQESFNLQAIHDVVYHQLDLDKYDHHEFPGVVPRTFLGPIFIAALSSPAIYILSLLKMSKFYSQLIVRGSLGLSVIYTLWKLQKEVRKQFGATTSTVFCLITVTQFHLMFYCTRTLPNVFALPFVLLALTFWIQQKQRPFIWFSALAIIVFRSELAIFLGLMLLVTFLTKRISVLKILSHAVPAGFFWLGLTVAVDSLFWRQLVWPEGKVLWYNTILNKSSNWGTSPFFWYFYSALPRALGCSIVFVPLGAAEKRTRILLLPALGFIFLYSFLPHKELRFIIYTFPVFNIVAAKVCSRILNNYRKSWLYKLGSLFVVMHLLVNAAYSGTSLYVSHFNYPGGVAIQKLHELVPSTAEVSVHIDVAAAQTGVSRFLEINSDWRYDKREDVKPGDQLMFSYTHILMETNPLQISHYKTTHRPLANIPGISKIGLNLTALPPFTLNLKPKLVLLEKLPLSS

Source

organism	Gallus gallus
common_name	chicken
ncbi_taxonomy_id	9031
host_organism	Homo sapiens

Entity 2 polymer

description	Gg12-11 Fab heavy chain
formula_weight	25119.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSYSSIHWVRQAPGKGLEWVASISSYYGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYYWDWWRGGWAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 polymer

description	Gg12-11 Fab light chain
formula_weight	23346.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYDPITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 non-polymer

description	[(3S,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] dihydrogen phosphate
formula_weight	440.6 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	;[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-5-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{S},4~{S},5~{R},6~{R})-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[[(2~{S},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,5-bis(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-6-(hydroxymethyl)-4-oxidanyl-oxan-2-yl] [oxidanyl-[(3~{S},6~{Z},10~{E},14~{E})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphoryl] hydrogen phosphate ;
formula_weight	2061.9 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

Entity 7 non-polymer

description	Lauryl Maltose Neopentyl Glycol
formula_weight	1005.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	85

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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	triclinic

resolution	2.42 Å
resolution_method	—
num_particles	580115

fit	/app/data/saxs_computation/s6/9s6t/9s6t.fit
pddf	/app/data/pr_computation/s6/9s6t/9s6t.pr.out
profile	/app/data/saxs_computation/s6/9s6t/9s6t.dat

Ternary cryo-EM structure of chicken ALG12 with Dol25-PP-GlcNAc2Man7, Dol25-P-Man, and Fab

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 (8)

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

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)