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9vni

Structure of the RhoA Y42C mutant featuring Thr37 coordination of magnesium ion

Method: X-RAY DIFFRACTION D_max: 59.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vni
deposition_date	2025-06-30
title	Structure of the RhoA Y42C mutant featuring Thr37 coordination of magnesium ion
keywords	Small GTPase, Y42C mutant, GDP bound, CELL INVASION; CELL INVASION
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	16.90 Å
rg_electron	15.73 Å
i0	7827430.00
molecular_weight	20025.0 kDa
excluded_volume	24892 Å³
envelope_volume	28208 Å³
shell_volume	15031 Å³
envelope_diameter	61.3 Å
shell_rg	21.94 Å
envelope_rg	16.29 Å
shape_rg	15.74 Å
total_rg	16.77 Å
total_atoms	1399
n_residues	174
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	59.4 Å
rg_real	16.84 Å
rg_real_error	0.37 Å
i0_real	7.8270e+06
i0_real_error	8.8440e+04
rg_reciprocal	16.85 Å
i0_reciprocal	7827000.0000
total_estimate	0.7716
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	52.4 Å
skewness	0.284
kurtosis	-0.123
angular_range	— – 0.4700 Å⁻¹
current_alpha	0.0000
highest_alpha	2066000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.679; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Transforming protein RhoA
formula_weight	20464.5 kDa
ec_number	3.6.5.2
mutation	Y42C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1504

GMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENCVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	99

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6. Citations (1)

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length_a	31.790 Å
length_b	63.430 Å
length_c	81.840 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	—

resolution	1.830 Å
resolution_low	28.420 Å
r_factor	0.2001
r_work	0.1948
r_free	0.2471

fit	/app/data/saxs_computation/vn/9vni/9vni.fit
pddf	/app/data/pr_computation/vn/9vni/9vni.pr.out
profile	/app/data/saxs_computation/vn/9vni/9vni.dat

Structure of the RhoA Y42C mutant featuring Thr37 coordination of magnesium ion

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