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9qh8

reduced NorQ-NorD VWA domain complex from Paracoccus denitrificans

Method: ELECTRON MICROSCOPY D_max: 112.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qh8
deposition_date	2025-03-14
title	reduced NorQ-NorD VWA domain complex from Paracoccus denitrificans
keywords	AAA+ Protein, MoxR, VWA domain, Nitric Oxide Reductase, CHAPERONE; CHAPERONE
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	36.98 Å
rg_electron	36.07 Å
i0	459469000.00
molecular_weight	172550.0 kDa
excluded_volume	215840 Å³
envelope_volume	294850 Å³
shell_volume	65793 Å³
envelope_diameter	113.8 Å
shell_rg	44.26 Å
envelope_rg	35.11 Å
shape_rg	36.07 Å
total_rg	36.61 Å
total_atoms	12182
n_residues	1785
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	112.9 Å
rg_real	36.71 Å
rg_real_error	0.64 Å
i0_real	4.5950e+08
i0_real_error	6.9600e+06
rg_reciprocal	36.88 Å
i0_reciprocal	459500000.0000
total_estimate	0.9001
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	49.9 Å
skewness	0.081
kurtosis	-0.526
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	174600000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protein NorQ
formula_weight	29450.7 kDa
mutation	E109Q
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	12182

MNAHVKTQGNGAVDAPFYLPQGDEVAVFEAAAANDLPVLLKGPTGCGKTRFVAHMAARLGRPLYTVACHDDLSAADLIGRYLLKGGETVWTDGPLTRAVREGAICYLDQVVEARKDVTVVLHPLTDDRRILPIDRTGEEIEAAPGFMLVASYNPGYQNILKTLKPSTRQRFVAMEFDFPEPAREVEIVARESGLDRDRTLGLVRLAGKIRGLKGQDLEEGVSTRLVVYAASLTRRGMNLDRAIEAAMIEPLTDDAEVKRGLRDLAAAIFG

Source

organism	Paracoccus denitrificans
ncbi_taxonomy_id	266
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	von Willebrand factor, type A
formula_weight	69927.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MGLDLEPWEPEETVGKIWHVWASSFGAPQAFEDQAVALSEVSGRLAVLFRALGGGAAVEIRPAAVQASHHRIGWLRRLGTPAETVPHASFDGEILRLPERLSVLPSRQANGALFLWLAACAAHGSLAPAQGDPLCRDLVRLGAAQRAVEATLQDAPGLTGLYDDLAELVLSLRPVAPLPPAEAVVEALARHLLGDPAPLPPLARDWLAMLDDPQVKAPRDYRPMRPVPLWPDLALPETTLAAAPGDAPDGIAADPANARMFRARRRQSDQPQRRDSLILHKFEALLSWADLMNLNRHVDDDDQDDAKKAAEDQEELGLGQVSKAPATRLRLHLDLAPEDADLEAVAGIRTYPEWDARRGRYLAHHVRVLENRAPEHDEALTPDPRAQTRIRAVRRQFEALRPGRLITTGHRDGDELDAELTVRAAADLRATGQGSDRIWRQSRPLARNLAVSILLDVSRSTESAVTGRAVIEIEREALAALAWGLDACGDRFAINAFSSLKRDRVFLSACKDFDEPMGAAIERRIAGLRPRFYTRLGAGIRHASAGLSAQASSRRLLLVITDGKPNDLDHYEGRHGIEDSAMAVREARRAGHAVHGITVDRDAKSWFPRIFGQGGFSLIPHPDRLLAALPVIYRQLVA

Source

organism	Paracoccus denitrificans
ncbi_taxonomy_id	266
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

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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	triclinic

resolution	3.80 Å
resolution_method	—
num_particles	51145

fit	/app/data/saxs_computation/qh/9qh8/9qh8.fit
pddf	/app/data/pr_computation/qh/9qh8/9qh8.pr.out
profile	/app/data/saxs_computation/qh/9qh8/9qh8.dat

reduced NorQ-NorD VWA domain complex from Paracoccus denitrificans

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)