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9qyo

Structural characterization of a mannose-binding site in human RNase2

Method: X-RAY DIFFRACTION D_max: 54.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qyo
deposition_date	2025-04-18
last_revision	2026-04-22
title	Structural characterization of a mannose-binding site in human RNase2
keywords	Monosaccharide, RNase2, Immune system, N-linked glycosylation, 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	16.32 Å
rg_electron	15.23 Å
i0	5898290.00
molecular_weight	16441.0 kDa
excluded_volume	20043 Å³
envelope_volume	22931 Å³
shell_volume	12942 Å³
envelope_diameter	52.1 Å
shell_rg	20.67 Å
envelope_rg	15.54 Å
shape_rg	15.20 Å
total_rg	16.23 Å
total_atoms	1156
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	54.2 Å
rg_real	16.25 Å
rg_real_error	0.30 Å
i0_real	5.8980e+06
i0_real_error	6.4850e+04
rg_reciprocal	16.26 Å
i0_reciprocal	5898000.0000
total_estimate	0.8938
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.2 Å
skewness	0.182
kurtosis	-0.484
angular_range	— – 0.4900 Å⁻¹
current_alpha	0.0000
highest_alpha	1348000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.995

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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	1457

MKPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVCGNPNMTCPSNKTRKNCHHSGSQVPLIHCNLTTPSPQNISNCRYAQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	alpha-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	beta-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	198

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6. Citations (1)

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length_a	41.806 Å
length_b	52.576 Å
length_c	56.864 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	1.020 Å
resolution_low	33.680 Å
r_factor	0.1335
r_work	0.1329
r_free	0.1487

fit	/app/data/saxs_computation/qy/9qyo/9qyo.fit
pddf	/app/data/pr_computation/qy/9qyo/9qyo.pr.out
profile	/app/data/saxs_computation/qy/9qyo/9qyo.dat