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9yx4

;Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA ;

Method: ELECTRON MICROSCOPY D_max: 209.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yx4
deposition_date	2025-10-26
title	;Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA ;
keywords	Carboxylase, transferase, lipid synthesis, mycolic acid synthesis, LIGASE; LIGASE
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	71.46 Å
rg_electron	71.47 Å
i0	18270900000.00
molecular_weight	747020.0 kDa
excluded_volume	717000 Å³
envelope_volume	1492200 Å³
shell_volume	177090 Å³
envelope_diameter	239.3 Å
shell_rg	69.49 Å
envelope_rg	70.44 Å
shape_rg	71.49 Å
total_rg	71.41 Å
total_atoms	56623
n_residues	7663
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	209.3 Å
rg_real	71.14 Å
rg_real_error	1.07 Å
i0_real	1.8210e+10
i0_real_error	3.6550e+08
rg_reciprocal	70.96 Å
i0_reciprocal	18250000000.0000
total_estimate	0.8570
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	95.1 Å
skewness	0.448
kurtosis	-0.129
angular_range	— – 0.1100 Å⁻¹
current_alpha	0.0147
highest_alpha	348400000.0000
n_real_points	23
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.466

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
formula_weight	63215.2 kDa
ec_number	6.3.4.14
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,I,J,K,L,Q,B,D,C,T,R,S
atom_count	56623

MANHASSKISKVLVANRGEIAVRVIRAAKDAGLASVAVYAEPDADAPHVRLADEAFALGGQTSAESYLVFEKILDAAEKSGANAIHPGYGFLSENADFAQAVIDAGLIWIGPSPQSIRDLGDKVTARHIAARAKAPLVPGTPDPVKDADEVVAFAKEHGVPVAIKAAFGGGGRGMKVARTLEEIPELFESATREAIAAFGRGECFVERYLDKPRHVEAQVIADQHGNVVVAGTRDCSLQRRFQKLVEEAPAPFLTDAQRKEIHESAKRICKEAGYYGAGTVEYLVGQDGLISFLEVNTRLQVEHPVTEETSGIDLVRQQFKIANGEPLDITEDPTPRGHSFEFRINGEDAGRGFLPAPGPVTKFVAPTGPGVRMDSGVETGSVIGGQFDSMLAKLIVTGATREEALERSRRALAEFTVEGLATVIPFHRAVVSDPAFIGDGEKFDVHTRWIETEWNNTVEPFTGGDPIEEEDTVPRQTVVVEVGGRRLEVSLPGDLAIGGGGGAAAPGVVRKKPKPRKRGGGGAKAASGDAVTAPMQGTVVKVAVEEGQEVSAGDLVVVLEAMKMENPVTAHKDGTITGLAVEAGAAITQGTVIAEIK

Entity 2 polymer

description	Acetyl-/propionyl-coenzyme A carboxylase AccE5
formula_weight	10357.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,P

MSGANDSTTVSGEVQADVTDEAKADHEAHIKVLRGEPTPEEMAALMAVLASAGGGPAEPVKKERNMWGHPVDKLRYSVFSWQRVTLLERTHMRR

Entity 3 polymer

description	Propionyl-CoA carboxylase beta chain
formula_weight	56234.1 kDa
ec_number	6.4.1.3
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,O

MTNKTTAELLAELREKLELAKEPGGEKAVAKREKKGIPSARARINALLDPGSFIEIGALAKTPGDPNALYGDGVVTGRGTIDGRPVGVFSHDQTVFQGSVGEMFGRKVARLMEWVAMVGCPIIGINDSAGARIQDAVTSLAWYAELGRRHEMLRGLVPEISLIFGKCAGGAVYSPIQTDLLVAVRDQGYMFITGPDVIKDVTGEDVTFDELGGADEQAKRGNIHKVVNSEAEAYQYVRDYLSFLPSNHFDNPPIVNPGMEPEITPHDLELDSIVPDADNMAYDMHEILLRIFDDGDVFEIAEQRGPAMITAFARVDGHPVGVIANQPMVLSGAIDNEASDKAASFIRFCDSYNLPLVFVVDTPGAMPGVAEEKGGIIKRGGRFFNAIVEADVPKVTVIIRKAYGGGYAVMGSKQLSADLNFAWPTARIAVIGAEGAAQLLVKRFPDPNAPEVQKIRDDFIEGYNLNMATPWIAAERGYIDAVIQPHETRLLLRKSLRLLRDKQNGPKVQRKHGLLPL

Entity 4 polymer

description	Propionyl-CoA carboxylase beta chain
formula_weight	58488.1 kDa
ec_number	6.4.1.3
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	G,H,M,N

MTSVTEPSAEHQVDIHTTAGKLADLKRRTEETLHPVGEAAVDKVHAKGKLTARERILALLDEGSFVELDALAKHRSTNFGLEKNRPLGDGVITGYGTIDGRDVCIFSQDATVFGGSLGEVYGEKIVKVQELAIKTGRPLIGINDGAGARIQEGVVSLGLYSRIFHNNIKASGVIPQISLIMGAAAGGHVYSPALTDFVVMVDQTSQMFITGPDVIKTVTGEDVTMEELGGAHTHMAKSGTAHYVASGEQDAFDYVRDLLSYLPPNNYADPPLYPVAIPEGSIEETLTDEDLELDTLIPDSPNQPYDMHEVITRILDDDEFLEVQAGYAGNIVVGFGRVEGRPVGIVANQPTQFAGCLDINASEKAARFIRTCDCFNIPIVLLVDVPGFLPGTDQEYNGIIRRGAKLLYAYGEATVAKVTVITRKSYGGAYCVMGSKDMGADVVVAWPTAQIAVMGASGAVGFVYRQQLKEAAKNGEDVDALRLELQQTYEDTLVNPYIAAERGYVDAVIPPSHTRGYVANALRLLERKIVQMPPKKHGNIPL

Entity 5 non-polymer

description	BIOTIN
formula_weight	244.3 kDa
src_method	syn
entity_count	6

Entity 6 non-polymer

description	BICARBONATE ION
formula_weight	61.0 kDa
src_method	syn
entity_count	8

Entity 7 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	8

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	8

Entity 9 non-polymer

description	;S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name) ;
formula_weight	1056.0 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	propionyl Coenzyme A
formula_weight	823.6 kDa
src_method	syn
entity_count	4

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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	2.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.30 Å
resolution_method	—
num_particles	124481

fit	/app/data/saxs_computation/yx/9yx4/9yx4.fit
pddf	/app/data/pr_computation/yx/9yx4/9yx4.pr.out
profile	/app/data/saxs_computation/yx/9yx4/9yx4.dat

;Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA ;

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

EM 3D

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)