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9r11

Structure of the PRYSPRY domain of human MID2, crystal form II

Method: X-RAY DIFFRACTION D_max: 68.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r11
deposition_date	2025-04-24
last_revision	2025-09-10
title	Structure of the PRYSPRY domain of human MID2, crystal form II
keywords	TRIM family, MID2, TRIM1, B30.2 DOMAIN, SPRY DOMAIN, PRYSPRY DOMAIN, E3 ubiquitin ligase, LIGASE; LIGASE
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	21.36 Å
rg_electron	20.44 Å
i0	22515700.00
molecular_weight	36798.0 kDa
excluded_volume	46217 Å³
envelope_volume	52914 Å³
shell_volume	21778 Å³
envelope_diameter	69.2 Å
shell_rg	26.60 Å
envelope_rg	20.53 Å
shape_rg	20.44 Å
total_rg	21.28 Å
total_atoms	2590
n_residues	330
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	68.9 Å
rg_real	21.31 Å
rg_real_error	0.37 Å
i0_real	2.2520e+07
i0_real_error	2.9360e+05
rg_reciprocal	21.32 Å
i0_reciprocal	22520000.0000
total_estimate	0.7273
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	25.3 Å
skewness	0.313
kurtosis	-0.391
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	6645000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 0.281; Positv: 1.000; Valcen: 0.998; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Probable E3 ubiquitin-protein ligase MID2
formula_weight	21597.6 kDa
ec_number	2.3.2.27
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	2920

SMNSQPFKLDPKMTHKKLKISNDGLQMEKDESSLKKSHTPERFSGTGCYGAAGNIFIDSGCHYWEVVMGSSTWYAIGIAYKSAPKNEWIGKNASSWVFSRCNSNFVVRHNNKEMLVDVPPHLKRLGVLLDYDNNMLSFYDPANSLHLHTFDVTFILPVCPTFTIWNKSLMILSGLPAPDFIDYPERQECN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	297

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6. Citations (1)

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length_a	53.406 Å
length_b	60.919 Å
length_c	118.590 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.640 Å
resolution_low	48.700 Å
r_factor	0.1579
r_work	0.1553
r_free	0.2057

fit	/app/data/saxs_computation/r1/9r11/9r11.fit
pddf	/app/data/pr_computation/r1/9r11/9r11.pr.out
profile	/app/data/saxs_computation/r1/9r11/9r11.dat

Structure of the PRYSPRY domain of human MID2, crystal form II

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