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9vnh

Structure of wild-type RhoA in complex with GDP and magnesium ion

Method: X-RAY DIFFRACTION D_max: 59.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vnh
deposition_date	2025-06-30
title	Structure of wild-type RhoA in complex with GDP and magnesium ion
keywords	Small GTPase, RhoA, wild-type, 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	17.13 Å
rg_electron	15.96 Å
i0	8341620.00
molecular_weight	20683.0 kDa
excluded_volume	25691 Å³
envelope_volume	29293 Å³
shell_volume	15381 Å³
envelope_diameter	61.5 Å
shell_rg	22.09 Å
envelope_rg	16.49 Å
shape_rg	15.96 Å
total_rg	16.98 Å
total_atoms	1447
n_residues	179
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	59.3 Å
rg_real	17.05 Å
rg_real_error	0.44 Å
i0_real	8.3420e+06
i0_real_error	9.9300e+04
rg_reciprocal	17.06 Å
i0_reciprocal	8342000.0000
total_estimate	0.7763
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	21.9 Å
skewness	0.246
kurtosis	-0.188
angular_range	— – 0.4650 Å⁻¹
current_alpha	0.0000
highest_alpha	2065000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; 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	20524.5 kDa
ec_number	3.6.5.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1606

GMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA

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	153

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6. Citations (1)

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length_a	31.870 Å
length_b	63.770 Å
length_c	82.780 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	1.790 Å
resolution_low	22.540 Å
r_factor	0.1838
r_work	0.1785
r_free	0.2313

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

Structure of wild-type RhoA in complex with GDP and 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