SAXSdb — 9vbg

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1. Structure Basics

entry_id	9vbg
deposition_date	2025-06-04
title	Cryo-EM structure of human PLD3 apo form
keywords	Exonuclease, IMMUNE SYSTEM; 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	33.95 Å
rg_electron	33.33 Å
i0	151438000.00
molecular_weight	97604.0 kDa
excluded_volume	121580 Å³
envelope_volume	152480 Å³
shell_volume	38557 Å³
envelope_diameter	119.9 Å
shell_rg	39.60 Å
envelope_rg	33.52 Å
shape_rg	33.30 Å
total_rg	33.91 Å
total_atoms	6870
n_residues	838
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	111.2 Å
rg_real	34.10 Å
rg_real_error	1.07 Å
i0_real	1.5140e+08
i0_real_error	2.5380e+06
rg_reciprocal	34.01 Å
i0_reciprocal	151400000.0000
total_estimate	0.7835
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.1 Å
skewness	0.440
kurtosis	-0.535
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	50620000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.772; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.877; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;5'-3' exonuclease PLD3 ;
formula_weight	48601.7 kDa
ec_number	3.1.16.1,3.1.4.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6870

EYGDLHLFGPNQRPAPCYDPCEAVLVESIPEGLDFPNASTGNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDTHTQEPSAQQGEEVLRQLQTLAPKGVNVRIAVSKPSGPQPQADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCSCLARDLTKIFEAYWFLGQAGSSIPSTWPRFYDTRYNQETPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQARIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQNGRGGLRSQLEAIFLRDWDSPYSHDLDTSADSVGNACRLLLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	2

Entity 3 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	2

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	4

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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	2.90 Å
resolution_method	—
num_particles	503473

fit	/app/data/saxs_computation/vb/9vbg/9vbg.fit
pddf	/app/data/pr_computation/vb/9vbg/9vbg.pr.out
profile	/app/data/saxs_computation/vb/9vbg/9vbg.dat

Cryo-EM structure of human PLD3 apo form

SAXS Profile

P(r) Distribution