← Back to search

9rbz

DvhD, HD-GYP domain, c-di-GMP-bound

Method: X-RAY DIFFRACTION D_max: 123.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rbz
deposition_date	2025-05-27
title	DvhD, HD-GYP domain, c-di-GMP-bound
keywords	Biofilm regulator, second messenger signaling, transmembrane, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	35.28 Å
rg_electron	35.46 Å
i0	143977000.00
molecular_weight	92619.0 kDa
excluded_volume	114550 Å³
envelope_volume	147240 Å³
shell_volume	36933 Å³
envelope_diameter	125.3 Å
shell_rg	38.74 Å
envelope_rg	35.68 Å
shape_rg	35.45 Å
total_rg	35.71 Å
total_atoms	6501
n_residues	823
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

▼

3. P(r) Analysis (GNOM)

dmax	123.0 Å
rg_real	35.63 Å
rg_real_error	1.16 Å
i0_real	1.4400e+08
i0_real_error	2.7120e+06
rg_reciprocal	35.42 Å
i0_reciprocal	143900000.0000
total_estimate	0.8078
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	30.1 Å
skewness	0.567
kurtosis	-0.298
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	65740000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.712; Smooth: 0.685

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	HD domain/sensory box protein
formula_weight	22795.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7215

DITELVDAQERSRKLVQQTIDAFITAIETKAPYLAGHSRGMSQFATAIARQMGLGERDVATVETAANLSQVGKIYVPSRLLTKPGALTAEEKAIVEEHVLHARRTLEHIEFDLPILDAIVQMNEHPDGTGYPEHLKGDAIGIHARILAVANAFCAMVRPRSYRPALGVDAVIGVLRKEGGSFDAGVVDALARLLASPAGERLLESLDVRQG

Source

organism	Nitratidesulfovibrio vulgaris str. Hildenborough
ncbi_taxonomy_id	882
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ;
formula_weight	690.4 kDa
src_method	syn
entity_count	6

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	635

▶

6. Citations (1)

▶

length_a	44.927 Å
length_b	44.939 Å
length_c	115.605 Å
angle_alpha	89.89 °
angle_beta	101.41 °
angle_gamma	96.21 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.800 Å
resolution_low	43.770 Å
r_factor	0.1921
r_work	0.1911
r_free	0.2285

fit	/app/data/saxs_computation/rb/9rbz/9rbz.fit
pddf	/app/data/pr_computation/rb/9rbz/9rbz.pr.out
profile	/app/data/saxs_computation/rb/9rbz/9rbz.dat

DvhD, HD-GYP domain, c-di-GMP-bound

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