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9qr7

Structural characterization of a N-acetylmuramic acid-binding site in human RNase2

Method: X-RAY DIFFRACTION D_max: 52.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qr7
deposition_date	2025-04-03
title	Structural characterization of a N-acetylmuramic acid-binding site in human RNase2
keywords	Monosaccharide, RNase2, Immune system, 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	16.19 Å
rg_electron	15.08 Å
i0	5855200.00
molecular_weight	16503.0 kDa
excluded_volume	20182 Å³
envelope_volume	22885 Å³
shell_volume	13015 Å³
envelope_diameter	51.1 Å
shell_rg	20.68 Å
envelope_rg	15.31 Å
shape_rg	15.04 Å
total_rg	16.16 Å
total_atoms	1150
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	52.2 Å
rg_real	16.11 Å
rg_real_error	0.29 Å
i0_real	5.8550e+06
i0_real_error	7.1390e+04
rg_reciprocal	16.12 Å
i0_reciprocal	5855000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	20.1 Å
skewness	0.183
kurtosis	-0.479
angular_range	— – 0.4900 Å⁻¹
current_alpha	0.0000
highest_alpha	1507000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	1463

MKPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVCGNPNMTCPSNKTRKNCHHSGSQVPLIHCNLTTPSPQNISNCRYAQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII

Source

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

Entity 2 non-polymer

description	N-acetyl-alpha-muramic acid
formula_weight	293.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	N-acetyl-beta-muramic acid
formula_weight	293.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	216

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6. Citations (1)

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length_a	41.674 Å
length_b	52.860 Å
length_c	56.439 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	1.010 Å
resolution_low	28.310 Å
r_factor	0.1329
r_work	0.1323
r_free	0.1489

fit	/app/data/saxs_computation/qr/9qr7/9qr7.fit
pddf	/app/data/pr_computation/qr/9qr7/9qr7.pr.out
profile	/app/data/saxs_computation/qr/9qr7/9qr7.dat