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9vbj

Cryo-EM structure of human PLD4 apo form

Method: ELECTRON MICROSCOPY D_max: 116.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vbj
deposition_date	2025-06-04
title	Cryo-EM structure of human PLD4 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	39.86 Å
rg_electron	38.73 Å
i0	525091000.00
molecular_weight	187450.0 kDa
excluded_volume	234660 Å³
envelope_volume	317230 Å³
shell_volume	66529 Å³
envelope_diameter	126.6 Å
shell_rg	46.25 Å
envelope_rg	37.95 Å
shape_rg	38.71 Å
total_rg	39.25 Å
total_atoms	13224
n_residues	1656
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	116.2 Å
rg_real	39.54 Å
rg_real_error	0.46 Å
i0_real	5.2510e+08
i0_real_error	7.8680e+06
rg_reciprocal	39.74 Å
i0_reciprocal	525200000.0000
total_estimate	0.8941
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.1 Å
skewness	0.001
kurtosis	-0.695
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0001
highest_alpha	211400000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.717

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	;5'-3' exonuclease PLD4 ;
formula_weight	46287.3 kDa
ec_number	3.1.16.1,3.1.4.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13224

RDSCQLVLVESIPQDLPSAAGSPSAQPLGQAWLQLLDTAQESVHVASYYWSLTGPDIGVNDSSSQLGEALLQKLQQLLGRNISLAVATSSPTLARTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCSHLAQDLEKTFQTYWVLGVPKAVLPKTWPQNFSSHFNRFQPFHGLFDGVPTTAYFSASPPALCPQGRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNTDPTMFPYLRSLQALSNPAANVSVDVKVFIVPVGNHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQSPGAQPAGATVQEQLRQLFERDWSSRYAVGLDGQAPGQDCVWQGLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 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	9

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	14

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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	3.31 Å
resolution_method	—
num_particles	121077

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