SAXSdb — 9yhn

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1. Structure Basics

entry_id	9yhn
deposition_date	2025-09-30
last_revision	2025-12-10
title	Hna Monomer
keywords	PD(D/E)XK nuclease. Superfamily 2 helicase. Anti-bacteriophage protein, IMMUNE SYSTEM; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

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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	29.35 Å
rg_electron	28.39 Å
i0	135624000.00
molecular_weight	92271.0 kDa
excluded_volume	115770 Å³
envelope_volume	145060 Å³
shell_volume	41412 Å³
envelope_diameter	94.5 Å
shell_rg	36.70 Å
envelope_rg	28.24 Å
shape_rg	28.39 Å
total_rg	29.19 Å
total_atoms	6493
n_residues	821
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	91.7 Å
rg_real	29.22 Å
rg_real_error	0.46 Å
i0_real	1.3560e+08
i0_real_error	1.7950e+06
rg_reciprocal	29.28 Å
i0_reciprocal	135600000.0000
total_estimate	0.8965
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	90.0 Å
skewness	0.218
kurtosis	-0.405
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	52480000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.909

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Helicase ATP-binding domain-containing protein
formula_weight	94841.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6493

MVDFRKRLGSTEAKKVVDPVALYETLDRATDKGPLRPAQEAVLGDWFKNYGGDVSGGSKRDVIIKLHTGQGKTLIGLLILQSRLNDNRRPCVYLCPDNFLIEQTCEQASQFGIKVSTVEDDLPDDFLAGKSILVTSVQKLFNGLTKFGLHRQSIEIDTILMDDAHACSDRIRDACKIKIPKDEPAYHALFKLFSTELELQGVGTFADLENGKRDALLPVPYWAWMAKEGEVAAILSAAADKKSIKFTWPLLKDRLRLCQCIFSGAALEIEPHIAPLEDFGSYARAKHRIFMSATVTDDSFLVKGLQLSPDTISNPLTYAKETWSGEKMVLIPSMMHEDLDRAKIVAWLAPVNPKLKFGIVALVPSFARNKDWGAYGAKTVDKDSVSEAVSDLKKGQYGTPLVLANRYDGIDLPDNTCRVLVFDSRPFSENLTDLYQEHCRPESEATLMRTIRSIEQGMGRSVRGEKDYSVVVAIGADLVRTLRDVSSRRYLSSQMATQIEIGLEIAEMAREEIAAGKEPLAALVGLINQCLKRDDGWKDFYADQMKKVAPKGANKEILELYSRELAAEQAYAAGDYNRAEQTIQKLLDDGLAHPDDRGWYLQERARYLHDGNRVEAQKLQVAAHRNNKLLLKPPTGVTVTKLTIVSQGRTERIANWVNKFESYADLDATVSDILGRLVFGTKAEKFESALNELAFALGFAGERPDAEWKEGPDNLWALNDIQYLLFECKSEVDTTRSEIHKRETEQMNRSAAWFDKHYLGMKVKRLIVHPANKIQSAAAFTHEVDGMLDSNLKAFVRSARAFFKSFENQNLKDLSVLHIQGLIDAHHLSVDNLINRYCSKLKNVK

Source

organism	Sinorhizobium meliloti
ncbi_taxonomy_id	382
host_organism	Escherichia coli

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.38 Å
resolution_method	—
num_particles	278967

fit	/app/data/saxs_computation/yh/9yhn/9yhn.fit
pddf	/app/data/pr_computation/yh/9yhn/9yhn.pr.out
profile	/app/data/saxs_computation/yh/9yhn/9yhn.dat

Hna Monomer

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)