SAXSdb — 9r2g

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1. Structure Basics

entry_id	9r2g
deposition_date	2025-04-30
title	Cytochrome bd II oxidase qOR-2 type from Mycobacterium smegmatis
keywords	MEMBRANE PROTEIN, ACTINOBACTERIA, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	27.60 Å
rg_electron	26.26 Å
i0	83090400.00
molecular_weight	81305.0 kDa
excluded_volume	105810 Å³
envelope_volume	120900 Å³
shell_volume	37068 Å³
envelope_diameter	94.9 Å
shell_rg	34.83 Å
envelope_rg	26.61 Å
shape_rg	26.26 Å
total_rg	27.25 Å
total_atoms	5759
n_residues	707
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	91.8 Å
rg_real	27.49 Å
rg_real_error	0.64 Å
i0_real	8.3090e+07
i0_real_error	1.1760e+06
rg_reciprocal	27.53 Å
i0_reciprocal	83090000.0000
total_estimate	0.8875
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.8 Å
skewness	0.226
kurtosis	-0.416
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	18480000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.967

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Cytochrome bd menaquinol oxidase subunit I
formula_weight	50327.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5774

MVFTETLLLLAADGEPPGLLPARQQMAFSLGWHIVLACFGVAFPTMIFVVHRRGIVRDDAVALGLAQRWAKVSAVLFAIGAVSGTVLSFEMGLLWPGLMGRFGDVLGLPFAFEGLSFFVEAIFLGIYLYGWGRMPPRRHLLTLIPMGLAGIVGTFCVVSVNAWMNNPAGFRIVNGEVVDIDPWRAMFNSGVWLQFAHMWVAAFMLVGLVVSGVYAFGMLRGRVDTHHRLGFAVPFTFASVAAVAQPLIGHVLGMRIHDTQPAKLAAFELAQTTEGPAPLRLGGVLIDGEVHWALTIPRLGSIIARNSLDAPVPGLDGVPRSDWPPVNITHLAFQSMVGIGTLLAAVAVVYWLARWRGRDLLANRWFLRLSVITGPLAVLAVESGWVATEVGRQPWTVWKVLTTTEAASQSSGLWWSYVIVLVVYLGMTIGAVVVLRSMARRWRAGETDLPSPYGPPRTEARS

Source

organism	Mycolicibacterium smegmatis
common_name	Mycobacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 2 polymer

description	Cytochrome bd-I oxidase subunit II
formula_weight	39166.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MTQATFVAMAMFLGVVIYALFAGADFGSGFYDLTAGDARSGAKVRTLVDHSIGPVWEANHVWLIYILVIWWTGFPRTFAAATTTLFIPLALALTGIVLRGASFAFRKYSATVSQARLFGAIFAASSLISPFFLGTVAGAIASGRVPAEGYGDRIGSWLNPTSLVGGFLAVATCVFLAGVFLTADAARSGDNGLADSLRRRTLAVGVVTGLIVFAGLYPVAHDAPTLTAGLRTYAAPLLVIALLAGVATVWLVFRRRYAISRIPAAVAVAAVVTGWGVGQYPWLLVDEVTIADAAGADATLTGLLIVVVLAGVIVLPALAYLLRLTQTEEWSRKLSGGSAENLYFQGWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Mycolicibacterium smegmatis
common_name	Mycobacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 3 non-polymer

description	CARDIOLIPIN
formula_weight	1464.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
formula_weight	632.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	HEME B/C
formula_weight	618.5 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	MENAQUINONE-9
formula_weight	785.2 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	7

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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	2.80 Å
resolution_method	—
num_particles	200084

fit	/app/data/saxs_computation/r2/9r2g/9r2g.fit
pddf	/app/data/pr_computation/r2/9r2g/9r2g.pr.out
profile	/app/data/saxs_computation/r2/9r2g/9r2g.dat

Cytochrome bd II oxidase qOR-2 type from Mycobacterium smegmatis

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)