SAXSdb — 9vbi

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1. Structure Basics

entry_id	9vbi
deposition_date	2025-06-04
title	Cryo-EM structure of PLD3 bound to ssDNA (poly(A))
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	33.60 Å
rg_electron	33.03 Å
i0	166077000.00
molecular_weight	100520.0 kDa
excluded_volume	124470 Å³
envelope_volume	155590 Å³
shell_volume	39506 Å³
envelope_diameter	118.4 Å
shell_rg	39.60 Å
envelope_rg	33.09 Å
shape_rg	33.01 Å
total_rg	33.60 Å
total_atoms	7066
n_residues	850
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	107.5 Å
rg_real	33.73 Å
rg_real_error	0.87 Å
i0_real	1.6610e+08
i0_real_error	3.0450e+06
rg_reciprocal	33.65 Å
i0_reciprocal	166100000.0000
total_estimate	0.8543
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.0 Å
skewness	0.429
kurtosis	-0.525
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	83920000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.919; Smooth: 0.674

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;DNA (5'-D(APAPAPAP*A)-3') ;
formula_weight	15302.2 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	C,B
atom_count	7066

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 2 polymer

description	;5'-3' exonuclease PLD3 ;
formula_weight	48467.5 kDa
ec_number	3.1.16.1,3.1.4.-
mutation	H201A/H416A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D

EYGDLHLFGPNQRPAPCYDPCEAVLVESIPEGLDFPNASTGNPSTSQAWLGLLAGAHSSLDIASFYWTLTNNDTHTQEPSAQQGEEVLRQLQTLAPKGVNVRIAVSKPSGPQPQADLQALLQSGAQVRMVDMQKLTHGVLATKFWVVDQTHFYLGSANMDWRSLTQVKELGVVMYNCSCLARDLTKIFEAYWFLGQAGSSIPSTWPRFYDTRYNQETPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLEFSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLAALRDNHTHSDIQVKLFVVPADEAQARIPYARVNANKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQNGRGGLRSQLEAIFLRDWDSPYSHDLDTSADSVGNACRLLLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 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	man
entity_count	4

Entity 4 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 5 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

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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	2.87 Å
resolution_method	—
num_particles	711544

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

Cryo-EM structure of PLD3 bound to ssDNA (poly(A))

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 branched

Entity 5 branched

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)