DvhD, PAS/HD-GYP domains

Method: X-RAY DIFFRACTION D_max: 100.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rc0
deposition_date	2025-05-27
title	DvhD, PAS/HD-GYP domains
keywords	Biofilm regulator, second messenger signaling, transmembrane, SIGNALING PROTEIN; SIGNALING PROTEIN
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	27.54 Å
rg_electron	27.38 Å
i0	17339200.00
molecular_weight	31501.0 kDa
excluded_volume	39325 Å³
envelope_volume	55587 Å³
shell_volume	18236 Å³
envelope_diameter	104.7 Å
shell_rg	32.24 Å
envelope_rg	27.00 Å
shape_rg	27.40 Å
total_rg	27.93 Å
total_atoms	2219
n_residues	296
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	100.0 Å
rg_real	27.87 Å
rg_real_error	1.11 Å
i0_real	1.7340e+07
i0_real_error	2.7320e+05
rg_reciprocal	27.78 Å
i0_reciprocal	17340000.0000
total_estimate	0.7494
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.4 Å
skewness	0.469
kurtosis	-0.557
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	3240000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.458; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.389; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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6. Citations (1)

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length_a	120.931 Å
length_b	120.931 Å
length_c	98.395 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	hexagonal

resolution	3.440 Å
resolution_low	46.230 Å
r_factor	0.3170
r_work	0.3155
r_free	0.3294

description	HD domain/sensory box protein
formula_weight	35692.5 kDa
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2219

DvhD, PAS/HD-GYP domains

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

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/rc/9rc0/9rc0.fit
pddf	/app/data/pr_computation/rc/9rc0/9rc0.pr.out
profile	/app/data/saxs_computation/rc/9rc0/9rc0.dat