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9r6d

Structural characterization of a trehalose-binding site in human RNase2

Method: X-RAY DIFFRACTION D_max: 50.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r6d
deposition_date	2025-05-11
last_revision	2026-04-22
title	Structural characterization of a trehalose-binding site in human RNase2
keywords	Disaccharide, RNase2, Immune system, Trehalose, PROTEIN BINDING; PROTEIN BINDING
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	16.15 Å
rg_electron	15.05 Å
i0	5519960.00
molecular_weight	16194.0 kDa
excluded_volume	19882 Å³
envelope_volume	22294 Å³
shell_volume	12749 Å³
envelope_diameter	49.5 Å
shell_rg	20.53 Å
envelope_rg	15.26 Å
shape_rg	15.03 Å
total_rg	16.09 Å
total_atoms	1126
n_residues	135
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	50.9 Å
rg_real	16.08 Å
rg_real_error	0.23 Å
i0_real	5.5200e+06
i0_real_error	5.5560e+04
rg_reciprocal	16.08 Å
i0_reciprocal	5520000.0000
total_estimate	0.9091
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	19.9 Å
skewness	0.164
kurtosis	-0.527
angular_range	— – 0.4950 Å⁻¹
current_alpha	0.0000
highest_alpha	1242000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 1.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Non-secretory ribonuclease
formula_weight	15611.8 kDa
ec_number	4.6.1.18
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1433

MKPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVCGNPNMTCPSNKTRKNCHHSGSQVPLIHCNLTTPSPQNISNCRYAQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII

Source

organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;
ncbi_taxonomy_id	866768
host_organism	Expression vector pET-mod

Entity 2 branched

description	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	199

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6. Citations (1)

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length_a	42.002 Å
length_b	52.527 Å
length_c	56.800 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	0.940 Å
resolution_low	38.560 Å
r_factor	0.1392
r_work	0.1389
r_free	0.1479

fit	/app/data/saxs_computation/r6/9r6d/9r6d.fit
pddf	/app/data/pr_computation/r6/9r6d/9r6d.pr.out
profile	/app/data/saxs_computation/r6/9r6d/9r6d.dat