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9uyv

Crystal Structure of VPS25 from Candidatus Prometheoarchaeum syntrophicum strain MK-D1

Method: X-RAY DIFFRACTION D_max: 84.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uyv
deposition_date	2025-05-15
last_revision	2026-06-03
title	Crystal Structure of VPS25 from Candidatus Prometheoarchaeum syntrophicum strain MK-D1
keywords	ESCRT-II, PROTEIN TRANSPORT; PROTEIN TRANSPORT
method	X-RAY DIFFRACTION

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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	26.76 Å
rg_electron	25.87 Å
i0	26866000.00
molecular_weight	43034.0 kDa
excluded_volume	55203 Å³
envelope_volume	72459 Å³
shell_volume	23856 Å³
envelope_diameter	91.8 Å
shell_rg	32.66 Å
envelope_rg	25.09 Å
shape_rg	25.82 Å
total_rg	26.93 Å
total_atoms	3042
n_residues	357
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	84.3 Å
rg_real	26.67 Å
rg_real_error	0.58 Å
i0_real	2.6870e+07
i0_real_error	3.8720e+05
rg_reciprocal	26.70 Å
i0_reciprocal	26870000.0000
total_estimate	0.8948
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	40.0 Å
skewness	0.135
kurtosis	-0.509
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	8865000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	ESCRT-II complex subunit
formula_weight	23111.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3816

MIALEEEVASETLIAEKSPYEKLIELHEWIELPQYGFMYSVPNKKKNKDDYMSWRDEWSQVLLDYAKVGTFHIIFLKRLLTEKPFNKFIDRKNAINELAEGLVEKNLGKWIKKKEALRVYWKSIEEWVSVIEKWAQDHAIFDVIMIPDIRNSDQEFAALPVEDLREIFKKIEKQGKADMVEIDKDQFGIKFKFS

Source

organism	Promethearchaeum sp.
ncbi_taxonomy_id	3061966
host_organism	Escherichia coli

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	687

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6. Citations (1)

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length_a	41.722 Å
length_b	61.130 Å
length_c	88.200 Å
angle_alpha	90.00 °
angle_beta	91.08 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.500 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.1740
r_free	0.1990

fit	/app/data/saxs_computation/uy/9uyv/9uyv.fit
pddf	/app/data/pr_computation/uy/9uyv/9uyv.pr.out
profile	/app/data/saxs_computation/uy/9uyv/9uyv.dat

Crystal Structure of VPS25 from Candidatus Prometheoarchaeum syntrophicum strain MK-D1

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

Refinement

Diffraction