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9vlb

Crystal Structure of a GDP-bound Bombyx mori RabX6

Method: X-RAY DIFFRACTION D_max: 79.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vlb
deposition_date	2025-06-25
last_revision	2025-12-10
title	Crystal Structure of a GDP-bound Bombyx mori RabX6
keywords	Rab, ras-related protein, 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	23.49 Å
rg_electron	22.76 Å
i0	24598400.00
molecular_weight	37033.0 kDa
excluded_volume	46057 Å³
envelope_volume	57707 Å³
shell_volume	22015 Å³
envelope_diameter	83.2 Å
shell_rg	28.69 Å
envelope_rg	22.76 Å
shape_rg	22.77 Å
total_rg	23.52 Å
total_atoms	2595
n_residues	329
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	79.0 Å
rg_real	23.58 Å
rg_real_error	0.60 Å
i0_real	2.4600e+07
i0_real_error	3.1490e+05
rg_reciprocal	23.56 Å
i0_reciprocal	24600000.0000
total_estimate	0.7925
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.3 Å
skewness	0.442
kurtosis	-0.309
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	6493000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ras-related protein Rab7
formula_weight	20038.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2605

MAVVKTPVLKVILCGEYGVGKSSLFRRFINNTFVPNSDRRATLGLDHFEKLYQVADKDVKLQLWDTGGMERIASVTSSYYKFAEAAILVFSLDNASSFHILSQHLLEIVSYAENAKIFLCGNKSDLEGASPQVTDADIETFCEQCHNLVNSTYKTSCKTGKGIEEMFADIALQRVEANRS

Source

organism	Bombyx mori
common_name	domestic silkworm
ncbi_taxonomy_id	7091
host_organism	Escherichia coli

Entity 2 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	5

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	10

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6. Citations (1)

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length_a	77.593 Å
length_b	109.735 Å
length_c	40.760 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	3.100 Å
resolution_low	44.800 Å
r_factor	0.2387
r_work	0.2359
r_free	0.2912

fit	/app/data/saxs_computation/vl/9vlb/9vlb.fit
pddf	/app/data/pr_computation/vl/9vlb/9vlb.pr.out
profile	/app/data/saxs_computation/vl/9vlb/9vlb.dat

Crystal Structure of a GDP-bound Bombyx mori RabX6

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