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9y5x

Crystal structure of shorter construct of SHP2 unbound N-SH2 domain

Method: X-RAY DIFFRACTION D_max: 45.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y5x
deposition_date	2025-09-05
last_revision	2026-01-07
title	Crystal structure of shorter construct of SHP2 unbound N-SH2 domain
keywords	SHP2, phosphatase, SH2, allostery, 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	14.60 Å
rg_electron	12.99 Å
i0	3336670.00
molecular_weight	12274.0 kDa
excluded_volume	15140 Å³
envelope_volume	16949 Å³
shell_volume	11127 Å³
envelope_diameter	42.4 Å
shell_rg	18.66 Å
envelope_rg	13.23 Å
shape_rg	12.95 Å
total_rg	14.31 Å
total_atoms	1695
n_residues	104
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	45.2 Å
rg_real	14.47 Å
rg_real_error	0.21 Å
i0_real	3.3370e+06
i0_real_error	3.2360e+04
rg_reciprocal	14.48 Å
i0_reciprocal	3337000.0000
total_estimate	0.8922
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.0 Å
skewness	0.011
kurtosis	-0.419
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	506600.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Isoform 1 of Tyrosine-protein phosphatase non-receptor type 11
formula_weight	11811.3 kDa
ec_number	3.1.3.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1863

GSHMRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	50

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6. Citations (2)

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length_a	63.271 Å
length_b	63.271 Å
length_c	76.284 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	1.800 Å
resolution_low	31.640 Å
r_factor	0.2133
r_work	0.2114
r_free	0.2500

fit	/app/data/saxs_computation/y5/9y5x/9y5x.fit
pddf	/app/data/pr_computation/y5/9y5x/9y5x.pr.out
profile	/app/data/saxs_computation/y5/9y5x/9y5x.dat