SAXSdb — 9qhd

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1. Structure Basics

entry_id	9qhd
deposition_date	2025-03-15
title	NorQD complex state 1 from Jhaorihella thermophila
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	37.44 Å
rg_electron	36.60 Å
i0	538263000.00
molecular_weight	189020.0 kDa
excluded_volume	237250 Å³
envelope_volume	322790 Å³
shell_volume	70228 Å³
envelope_diameter	117.8 Å
shell_rg	45.36 Å
envelope_rg	35.75 Å
shape_rg	36.59 Å
total_rg	37.21 Å
total_atoms	13295
n_residues	1791
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	115.0 Å
rg_real	37.15 Å
rg_real_error	0.57 Å
i0_real	5.3830e+08
i0_real_error	7.4970e+06
rg_reciprocal	37.33 Å
i0_reciprocal	538400000.0000
total_estimate	0.8973
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.3 Å
skewness	0.083
kurtosis	-0.518
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	232300000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.953

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Nitric oxide reductase NorQ protein
formula_weight	29382.7 kDa
mutation	E107Q
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	13295

MDGSTTFGGAATAPFYLPQADECEVFAAAHENDLPVLLKGPTGCGKTRFVAHMAQRLGRKLYTVACHDDLAAADLIGRYLLKGGETVWVDGPLTRAVREGAICYLDQVVEARKDVTVVLHPLTDDRRILPIDRTGEELEAAPGFMLVASYNPGYQNILKTLKPSTRQRFISIEFDFPHPDLETEVVAQESGLPLERCKPLIRLANKLRALKGQDLEEGVSTRLVVYAATLIAQGMNTDRAIRAAMIEPLTDDEDVKRGLLDLVTAVFG

Source

organism	Jhaorihella thermophila
ncbi_taxonomy_id	488547
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Nitric oxide reductase NorD protein
formula_weight	71726.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MDRIEFEPWEPEETVGKLWHKFASRLDAPEAHEGAAVDLSEIGGRLAVLFRGLGGASSVELRPVSPEISRHRLSWRRRLGAEAEAVPRASFDGEVLRLPDRLAVFPSREANGALYVWLAACAAHASDRVDQDDPLRADLAALAASRAMVAATLEDAPGLRPLYEGLCAALLHQRRVPDLPRDEAAVEAVIRNMLGDPAPLSDRAAAFQAACAGDPLDPAITAPRKYRPFRPVPLWPELRPVEFSEAGEVETREIEGTPEEAGEKTHRARRRKSDQAERRDSLILHKFEAILSWAEFLNLNRRVDDDDPDNAKKAADDQEEIGLGQISKAPPTRLKLHLDLAPEDVDRERLSGRITYPEWDTRTGAYLPDHVCVLTSDVEAKPEQEAYAHDPAASRRIRAVRRQFEALRPGRVTTRGHLDGDDLDIEAAVRAEVDRLASGEGSERIWLRSRPEARDLAVSILLDVSRSTESAVSGRAVIDIEREALDALAWGLDACGDDFAIHAFSSLKRHRVHVQRCKGFDEPMGPEVERRIGGLRPGFYTRLGAAIRHVSAELSQQARKRRLLLVITDGKPNDLDHYEGRHGIEDTAMAVREARRAGHSVFGITVDAKGKAWFSRMFGQGGFAVIPDPEKLIFALPQIYRQLVGA

Source

organism	Jhaorihella thermophila
ncbi_taxonomy_id	488547
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	3.30 Å
resolution_method	—
num_particles	265840

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

NorQD complex state 1 from Jhaorihella thermophila

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)